Methods of treatment using antibodies to neutrokine-alpha

ABSTRACT

The present invention relates to a novel Neutrokine-alpha, and a splice variant thereof designated Neutrokine-alphaSV, polynucleotides and polypeptides which are members of the TNF family. In particular, isolated nucleic acid molecules are provided encoding the human Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides, including soluble forms of the extracellular domain. Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides are also provided as are vectors, host cells and recombinant methods for producing the same. The invention further relates to screening methods for identifying agonists and antagonists of Neutrokine-alpha and/or Neutrokine-alphaSV activity. Also provided are diagnostic methods for detecting immune system-related disorders and therapeutic methods for treating immune system-related disorders.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of copending U.S. patent applicationSer. No. 12/170,333, filed Jul. 9, 2008, which is a continuation of U.S.patent application Ser. No. 11/382,837, filed May 11, 2006, nowabandoned, which is a continuation of U.S. application Ser. No.09/589,288, filed Jun. 8, 2000, currently pending, which is acontinuation of U.S. patent application Ser. No. 09/507,968, filed Feb.22, 2000, issued as U.S. Pat. No. 6,812,327 on Nov. 2, 2004. U.S. patentapplication Ser. No. 09/507,968, filed Feb. 22, 2000, issued as U.S.Pat. No. 6,812,327 on Nov. 2, 2004, claims the benefit of priority under35 U.S.C. §119(e) of U.S. Provisional Application Nos. 60/122,388, filedMar. 2, 1999; 60/124,097, filed Mar. 12, 1999; 60/126,599, filed Mar.26, 1999; 60/127,598, filed Apr. 2, 1999; 60/130,412, filed Apr. 16,1999; 60/130,696, filed Apr. 23, 1999; 60/131,278, filed Apr. 27, 1999;60/131,673, filed Apr. 29, 1999; 60/136,784, filed May 28, 1999;60/142,659, filed Jul. 6, 1999; 60/145,824, filed Jul. 27, 1999;60/167,239, filed Nov. 24, 1999; 60/168,624, filed Dec. 3, 1999;60/171,108, filed Dec. 16, 1999; 60/171,626, filed Dec. 23, 1999; and60/176,015, filed Jan. 14, 2000. U.S. patent application Ser. No.09/507,968, filed Feb. 22, 2000, issued as U.S. Pat. No. 6,812,327 onNov. 2, 2004, is a continuation-in-part of U.S. patent application Ser.No. 09/255,794, filed Feb. 23, 1999, issued as U.S. Pat. No. 6,716,576on Apr. 6, 2004, which is a continuation-in-part of U.S. patentapplication Ser. No. 09/005,874, filed Jan. 12, 1998, issued as U.S.Pat. No. 6,689,579 on Feb. 10, 2004, which is a continuation-in-part ofInternational Patent Application No. PCT/US96/17957, filed Oct. 25,1996. U.S. patent application Ser. No. 09/005,874, filed Jan. 12, 1998,issued as U.S. Pat. No. 6,689,579 on Feb. 10, 2004, claims the benefitof priority under 35 U.S.C. §119(e) of U.S. Provisional Application No.60/036,100, filed Jan. 14, 1997. Each of the aforementionednon-provisional and provisional applications is hereby incorporated byreference in its entirety.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY

Incorporated by reference in its entirety herein is a computer-readablenucleotide/amino acid sequence listing submitted concurrently herewithand identified as follows: One 48,779 Byte ASCII (Text) file named“SequenceListing.TXT,” created on Jul. 26, 2010.

BACKGROUND OF THE INVENTION

The present invention relates to a novel cytokine which has beendesignated Neutrokine-alpha (“Neutrokine-alpha”). In addition, anapparent splicing variant of Neutrokine-alpha has been identified anddesignated Neutrokine-alphaSV. In specific embodiments, the presentinvention provides nucleic acid molecules encoding Neutrokine-alpha andNeutrokine-alphaSV polypeptides. In additional embodiments,Neutrokine-alpha and Neutrokine-alphaSV polypeptides are also provided,as are vectors, host cells and recombinant methods for producing thesame.

RELATED ART

Human tumor necrosis factors (TNF-alpha) and (TNF-beta, or lymphotoxin)are related members of a broad class of polypeptide mediators, whichincludes the interferons, interleukins and growth factors, collectivelycalled cytokines (Beutler, B. and Cerami, A., Annu. Rev. Immunol.7:625-655 (1989)). Sequence analysis of cytokine receptors has definedseveral subfamilies of membrane proteins (1) the Ig superfamily, (2) thehematopoietin (cytokine receptor superfamily) and (3) the tumor necrosisfactor (TNF)/nerve growth factor (NGF) receptor superfamily (for reviewof TNF superfamily see, Gruss and Dower, Blood 85(12):3378-3404 (1995)and Aggarwal and Natarajan, Eur. Cytokine Netw., 7(2):93-124 (1996)).The TNF/NGF receptor superfamily contains at least 10 differentproteins. Gruss and Dower, supra. Ligands for these receptors have beenidentified and belong to at least two cytokine superfamilies. Gruss andDower, supra.

Tumor necrosis factor (a mixture of TNF-alpha and TNF-beta) wasoriginally discovered as a result of its anti-tumor activity, however,now it is recognized as a pleiotropic cytokine capable of numerousbiological activities including apoptosis of some transformed celllines, mediation of cell activation and proliferation and also asplaying important roles in immune regulation and inflammation.

To date, known members of the TNF-ligand superfamily include TNF-alpha,TNF-beta (lymphotoxin-alpha), LT-beta, OX40L, Fas ligand, CD30L, CD27L,CD40L and 4-IBBL. The ligands of the TNF ligand superfamily are acidic,TNF-like molecules with approximately 20% sequence homology in theextracellular domains (range, 12%-36%) and exist mainly asmembrane-bound forms with the biologically active form being atrimeric/multimeric complex. Soluble forms of the TNF ligand superfamilyhave only been identified so far for TNF, LT-beta, and Fas ligand (for ageneral review, see Gruss, H. and Dower, S. K., Blood, 85(12):3378-3404(1995)), which is hereby incorporated by reference in its entirety.These proteins are involved in regulation of cell proliferation,activation, and differentiation, including control of cell survival ordeath by apoptosis or cytotoxicity (Armitage, R. J., Curr. Opin.Immunol. 6:407 (1994) and Smith, C. A., Cell 75:959 (1994)).

Tumor necrosis factor-alpha (TNF-alpha; also termed cachectin;hereinafter “TNF”) is secreted primarily by monocytes and macrophages inresponse to endotoxin or other stimuli as a soluble homotrimer of 17 kDaprotein subunits (Smith, R. A. et al., J. Biol. Chem. 262:6951-6954(1987)). A membrane-bound 26 kD precursor form of TNF has also beendescribed (Kriegler, M. et al., Cell 53:45-53 (1988)).

Accumulating evidence indicates that TNF is a regulatory cytokine withpleiotropic biological activities. These activities include: inhibitionof lipoprotein lipase synthesis (“cachectin” activity) (Beutler, B. etal., Nature 316:552 (1985)), activation of polymorphonuclear leukocytes(Klebanoff, S. J. et al., J. Immunol. 136:4220 (1986); Perussia, B., etal., J. Immunol. 138:765 (1987)), inhibition of cell growth orstimulation of cell growth (Vilcek, J. et al., J. Exp. Med. 163:632(1986); Sugarman, B. J. et al., Science 230:943 (1985); Lachman, L. B.et al., J. Immunol. 138:2913 (1987)), cytotoxic action on certaintransformed cell types (Lachman, L. B. et al., supra; Darzynkiewicz, Z.et al., Canc. Res. 44:83 (1984)), antiviral activity (Kohase, M. et al.,Cell 45:659 (1986); Wong, G. H. W. et al., Nature 323:819 (1986)),stimulation of bone resorption (Bertolini, D. R. et al., Nature 319:516(1986); Saklatvala, J., Nature 322:547 (1986)), stimulation ofcollagenase and prostaglandin E2 production (Dayer, J.-M. et al., J.Exp. Med. 162:2163 (1985)); and immunoregulatory actions, includingactivation of T cells (Yokota, S. et al., J. Immunol. 140:531 (1988)), Bcells (Kehrl, J. H. et al., J. Exp. Med. 166:786 (1987)), monocytes(Philip, R. et al., Nature 323:86 (1986)), thymocytes (Ranges, G. E. etal., J. Exp. Med. 167:1472 (1988)), and stimulation of the cell-surfaceexpression of major histocompatibility complex (MHC) class I and classII molecules (Collins, T. et al., Proc. Natl. Acad. Sci. USA 83:446(1986); Pujol-Borrel, R. et al., Nature 326:304 (1987)).

TNF is noted for its pro-inflammatory actions which result in tissueinjury, such as induction of procoagulant activity on vascularendothelial cells (Pober, J. S. et al., J. Immunol. 136:1680 (1986)),increased adherence of neutrophils and lymphocytes (Pober, J. S. et al.,J. Immunol. 138:3319 (1987)), and stimulation of the release of plateletactivating factor from macrophages, neutrophils and vascular endothelialcells (Camussi, G. et al., J. Exp. Med. 166:1390 (1987)).

Recent evidence implicates TNF in the pathogenesis of many infections(Cerami, A. et al., Immunol. Today 9:28 (1988)), immune disorders,neoplastic pathology, e.g., in cachexia accompanying some malignancies(Oliff, A. et al., Cell 50:555 (1987)), and in autoimmune pathologiesand graft-versus host pathology (Piguet, P.-F. et al., J. Exp. Med.166:1280 (1987)). The association of TNF with cancer and infectiouspathologies is often related to the host's catabolic state. A majorproblem in cancer patients is weight loss, usually associated withanorexia. The extensive wasting which results is known as “cachexia”(Kern, K. A. et al. J. Parent. Enter. Nutr. 12:286-298 (1988)). Cachexiaincludes progressive weight loss, anorexia, and persistent erosion ofbody mass in response to a malignant growth. The cachectic state is thusassociated with significant morbidity and is responsible for themajority of cancer mortality. A number of studies have suggested thatTNF is an important mediator of the cachexia in cancer, infectiouspathology, and in other catabolic states.

TNF is thought to play a central role in the pathophysiologicalconsequences of Gram-negative sepsis and endotoxic shock (Michie, H. R.et al., Br. J. Surg. 76:670-671 (1989); Debets, J. M. H. et al., SecondVienna Shock Forum, p. 463-466 (1989); Simpson, S. Q. et al., Crit. CareClin. 5:27-47 (1989)), including fever, malaise, anorexia, and cachexia.Endotoxin is a potent monocyte/macrophage activator which stimulatesproduction and secretion of TNF (Kornbluth, S. K. et al., J. Immunol.137:2585-2591 (1986)) and other cytokines. Because TNF could mimic manybiological effects of endotoxin, it was concluded to be a centralmediator responsible for the clinical manifestations ofendotoxin-related illness. TNF and other monocyte-derived cytokinesmediate the metabolic and neurohormonal responses to endotoxin (Michie,H. R. et al., N. Eng. J. Med. 318:1481-1486 (1988)). Endotoxinadministration to human volunteers produces acute illness with flu-likesymptoms including fever, tachycardia, increased metabolic rate andstress hormone release (Revhaug, A. et al., Arch. Surg. 123:162-170(1988)). Elevated levels of circulating TNF have also been found inpatients suffering from Gram-negative sepsis (Waage, A. et al., Lancet1:355-357 (1987); Hammerle, A. F. et al., Second Vienna Shock Forum p.715-718 (1989); Debets, J. M. H. et al., Crit. Care Med. 17:489-497(1989); Calandra, T. et al., J. Infec. Dis. 161:982-987 (1990)).

Passive immunotherapy directed at neutralizing TNF may have a beneficialeffect in Gram-negative sepsis and endotoxemia, based on the increasedTNF production and elevated TNF levels in these pathology states, asdiscussed above. Antibodies to a “modulator” material which wascharacterized as cachectin (later found to be identical to TNF) weredisclosed by Cerami et al. (EPO Patent Publication 0,212,489, Mar. 4,1987). Such antibodies were said to be useful in diagnostic immunoassaysand in therapy of shock in bacterial infections. Rubin et al. (EPOPatent Publication 0,218,868, Apr. 22, 1987) disclosed monoclonalantibodies to human TNF, the hybridomas secreting such antibodies,methods of producing such antibodies, and the use of such antibodies inimmunoassay of TNF. Yone et al. (EPO Patent Publication 0,288,088, Oct.26, 1988) disclosed anti-TNF antibodies, including mAbs, and theirutility in immunoassay diagnosis of pathologies, in particularKawasaki's pathology and bacterial infection. The body fluids ofpatients with Kawasaki's pathology (infantile acute febrilemucocutaneous lymph node syndrome; Kawasaki, T., Allergy 16:178 (1967);Kawasaki, T., Shonica (Pediatrics) 26:935 (1985)) were said to containelevated TNF levels which were related to progress of the pathology(Yone et al., supra).

Other investigators have described mAbs specific for recombinant humanTNF which had neutralizing activity in vitro (Liang, C-M. et al.Biochem. Biophys. Res. Comm. 137:847-854 (1986); Meager, A. et al.,Hybridoma 6:305-311 (1987); Fendly et al., Hybridoma 6:359-369 (1987);Bringman, T S et al., Hybridoma 6:489-507 (1987); Hirai, M. et al., J.Immunol. Meth. 96:57-62 (1987); Moller, A. et al. (Cytokine 2:162-169(1990)). Some of these mAbs were used to map epitopes of human TNF anddevelop enzyme immunoassays (Fendly et al., supra; Hirai et al., supra;Moller et al., supra) and to assist in the purification of recombinantTNF (Bringman et al., supra). However, these studies do not provide abasis for producing TNF neutralizing antibodies that can be used for invivo diagnostic or therapeutic uses in humans, due to immunogenicity,lack of specificity and/or pharmaceutical suitability.

Neutralizing antisera or mAbs to TNF have been shown in mammals otherthan man to abrogate adverse physiological changes and prevent deathafter lethal challenge in experimental endotoxemia and bacteremia. Thiseffect has been demonstrated, e.g., in rodent lethality assays and inprimate pathology model systems (Mathison, J. C. et al., J. Clin.Invest. 81:1925-1937 (1988); Beutler, B. et al., Science 229:869-871(1985); Tracey, K. J. et al., Nature 330:662-664 (1987); Shimamoto, Y.et al., Immunol. Lett. 17:311-318 (1988); Silva, A. T. et al., J.Infect. Dis. 162:421-427 (1990); Opal, S. M. et al., J. Infect. Dis.161:1148-1152 (1990); Hinshaw, L. B. et al., Circ. Shock 30:279-292(1990)).

To date, experience with anti-TNF mAb therapy in humans has been limitedbut shows beneficial therapeutic results, e.g., in arthritis and sepsis.See, e.g., Elliott, M. J. et al., Baillieres Clin. Rheumatol. 9:633-52(1995); Feldmann M, et al., Ann. N.Y. Acad. Sci. USA 766:272-8 (1995);van der Poll, T. et al., Shock 3:1-12 (1995); Wherry et al., Crit. Care.Med. 21:S436-40 (1993); Tracey K. J., et al., Crit. Care Med. 21:S415-22(1993).

Mammalian development is dependent on both the proliferation anddifferentiation of cells as well as programmed cell death which occursthrough apoptosis (Walker, et al., Methods Achiev. Exp. Pathol. 13:18(1988). Apoptosis plays a critical role in the destruction of immunethymocytes that recognize self antigens. Failure of this normalelimination process may play a role in autoimmune diseases (Gammon etal., Immunology Today 12:193 (1991)).

Itoh et al. (Cell 66:233 (1991)) described a cell surface antigen,Fas/CD95 that mediates apoptosis and is involved in clonal deletion ofT-cells. Fas is expressed in activated T-cells, B-cells, neutrophils andin thymus, liver, heart and lung and ovary in adult mice(Watanabe-Fukunaga et al., J. Immunol. 148:1274 (1992)) in addition toactivated T-cells, B-cells, neutrophils. In experiments where amonoclonal Ab is cross-linked to Fas, apoptosis is induced (Yonehara etal., J. Exp. Med. 169:1747 (1989); Trauth et al., Science 245:301(1989)). In addition, there is an example where binding of a monoclonalAb to Fas is stimulatory to T-cells under certain conditions (Aldersonet al., J. Exp. Med. 178:2231 (1993)).

Fas antigen is a cell surface protein of relative MW of 45 kDa. Bothhuman and murine genes for Fas have been cloned by Watanabe-Fukunaga etal., (J. Immunol. 148:1274 (1992)) and Itoh et al. (Cell 66:233 (1991)).The proteins encoded by these genes are both transmembrane proteins withstructural homology to the Nerve Growth Factor/Tumor Necrosis Factorreceptor superfamily, which includes two TNF receptors, the low affinityNerve Growth Factor receptor and CD40, CD27, CD30, and OX40.

Recently the Fas ligand has been described (Suda et al., Cell 75:1169(1993)). The amino acid sequence indicates that Fas ligand is a type IItransmembrane protein belonging to the TNF family. Thus, the Fas ligandpolypeptide comprises three main domains: a short intracellular domainat the amino terminal end and a longer extracellular domain at thecarboxy terminal end, connected by a hydrophobic transmembrane domain.Fas ligand is expressed in splenocytes and thymocytes, consistent withT-cell mediated cytotoxicity. The purified Fas ligand has a MW of 40kDa.

Recently, it has been demonstrated that Fas/Fas ligand interactions arerequired for apoptosis following the activation of T-cells (Ju et al.,Nature 373:444 (1995); Brunner et al., Nature 373:441 (1995)).Activation of T-cells induces both proteins on the cell surface.Subsequent interaction between the ligand and receptor results inapoptosis of the cells. This supports the possible regulatory role forapoptosis induced by Fas/Fas ligand interaction during normal immuneresponses.

Accordingly, there is a need to provide cytokines similar to TNF thatare involved in pathological conditions. Such novel cytokines may beused to make novel antibodies or other antagonists that bind theseTNF-like cytokines for diagnosis and therapy of disorders related toTNF-like cytokines.

BRIEF SUMMARY OF THE INVENTION

In accordance with one embodiment of the present invention, there isprovided a novel extracellular domain of a Neutrokine-alpha polypeptide,and a novel extracellular domain of a Neutrokine-alphaSV polypeptide, aswell as biologically active and diagnostically or therapeutically usefulfragments, analogs and derivatives thereof.

In accordance with another embodiment of the present invention, thereare provided isolated nucleic acid molecules encoding humanNeutrokine-alpha or Neutrokine-alphaSV, including mRNAs, DNAs, cDNAs,genomic DNAs as well as analogs and biologically active anddiagnostically or therapeutically useful fragments and derivativesthereof.

The present invention provides isolated nucleic acid moleculescomprising, or alternatively, consisting of, a polynucleotide encoding acytokine and an apparent splice variant thereof that are structurallysimilar to TNF and related cytokines and have similar biological effectsand activities. This cytokine is named Neutrokine-alpha and theinvention includes Neutrokine-alpha polypeptides having at least aportion of the amino acid sequence in FIGS. 1A and 1B (SEQ ID NO:2) oramino acid sequence encoded by the cDNA clone (HNEDU15) deposited onOct. 22, 1996 assigned ATCC number 97768. The nucleotide sequencedetermined by sequencing the deposited Neutrokine-alpha clone, which isshown in FIGS. 1A and 1B (SEQ ID NO:1), contains an open reading frameencoding a complete polypeptide of 285 amino acid residues including anN-terminal methionine, a predicted intracellular domain of about 46amino acid residues, a predicted transmembrane domain of about 26 aminoacids, a predicted extracellular domain of about 213 amino acids, and adeduced molecular weight for the complete protein of about 31 kDa. Asfor other type II transmembrane proteins, soluble forms ofNeutrokine-alpha include all or a portion of the extracellular domaincleaved from the transmembrane domain and a polypeptide comprising thecomplete Neutrokine-alpha polypeptide lacking the transmembrane domain,i.e., the extracellular domain linked to the intracellular domain.

The apparent splice variant of Neutrokine-alpha is namedNeutrokine-alphaSV and the invention includes Neutrokine-alphaSVpolypeptides comprising, or alternatively, consisting of, at least aportion of the amino acid sequence in FIGS. 5A and 5B (SEQ ID NO:19) oramino acid sequence encoded by the cDNA clone HDPMC52 deposited on Dec.10, 1998 and assigned ATCC number 203518. The nucleotide sequencedetermined by sequencing the deposited Neutrokine-alphaSV clone, whichis shown in FIGS. 5A and 5B (SEQ ID NO:18), contains an open readingframe encoding a complete polypeptide of 266 amino acid residuesincluding an N-terminal methionine, a predicted intracellular domain ofabout 46 amino acid residues, a predicted transmembrane domain of about26 amino acids, a predicted extracellular domain of about 194 aminoacids, and a deduced molecular weight for the complete protein of about29 kDa. As for other type II transmembrane proteins, soluble forms ofNeutrokine-alphaSV include all or a portion of the extracellular domaincleaved from the transmembrane domain and a polypeptide comprising thecomplete Neutrokine-alphaSV polypeptide lacking the transmembranedomain, i.e., the extracellular domain linked to the intracellulardomain.

Thus, one embodiment of the invention provides an isolated nucleic acidmolecule comprising, or alternatively consisting of, a polynucleotidehaving a nucleotide sequence selected from the group consisting of: (a)a nucleotide sequence encoding a full-length Neutrokine-alphapolypeptide having the complete amino acid sequence in FIGS. 1A and 1B(SEQ ID NO:2) or as encoded by the cDNA clone contained in the deposithaving ATCC accession number 97768; (b) a nucleotide sequence encodingthe predicted extracellular domain of the Neutrokine-alpha polypeptidehaving the amino acid sequence at positions 73 to 285 in FIGS. 1A and 1B(SEQ ID NO:2) or as encoded by the clone contained in the deposit havingATCC accession number 97768; (c) a nucleotide sequence encoding afragment of the polypeptide of (b) having Neutrokine-alpha functionalactivity (e.g., biological activity); (d) a nucleotide sequence encodinga polypeptide comprising the Neutrokine-alpha intracellular domain(predicted to constitute amino acid residues from about 1 to about 46 inFIGS. 1A and 1B (SEQ ID NO:2)) or as encoded by the clone contained inthe deposit having ATCC accession number 97768; (e) a nucleotidesequence encoding a polypeptide comprising the Neutrokine-alphatransmembrane domain (predicted to constitute amino acid residues fromabout 47 to about 72 in FIGS. 1A and 1B (SEQ ID NO:2) or as encoded bythe cDNA clone contained in the deposit having ATCC accession number97768; (f) a nucleotide sequence encoding a soluble Neutrokine-alphapolypeptide having the extracellular and intracellular domains butlacking the transmembrane domain; and (g) a nucleotide sequencecomplementary to any of the nucleotide sequences in (a), (b), (c), (d),(e) or (f) above.

Further embodiments of the invention include isolated nucleic acidmolecules that comprise, or alternatively consist of, a polynucleotidehaving a nucleotide sequence at least 80%, 85% or 90% identical, andmore preferably at least 95%, 96%, 97%, 98% or 99% identical, to any ofthe nucleotide sequences in (a), (b), (c), (d), (e), (f) or (g) above,or a polynucleotide which hybridizes under stringent hybridizationconditions to a polynucleotide in (a), (b), (c), (d), (e), (f) or (g)above. This polynucleotide which hybridizes does not hybridize understringent hybridization conditions to a polynucleotide having anucleotide sequence consisting of only A residues or of only T residues.

Another embodiment of the invention provides an isolated nucleic acidmolecule comprising, or alternatively consisting of, a polynucleotidehaving a nucleotide sequence selected from the group consisting of: (a)a nucleotide sequence encoding a full-length Neutrokine-alphaSVpolypeptide having the complete amino acid sequence in FIGS. 5A and 5B(SEQ ID NO:19) or as encoded by the cDNA clone contained in the ATCCDeposit deposited on Dec. 10, 1998 as ATCC Number 203518; (b) anucleotide sequence encoding the predicted extracellular domain of theNeutrokine-alphaSV polypeptide having the amino acid sequence atpositions 73 to 266 in FIGS. 1A and 1B (SEQ ID NO:2) or as encoded bythe cDNA clone contained in ATCC 203518 deposited on Dec. 10, 1998; (c)a nucleotide sequence encoding a polypeptide comprising theNeutrokine-alphaSV intracellular domain (predicted to constitute aminoacid residues from about 1 to about 46 in FIGS. 5A and 5B (SEQ IDNO:19)) or as encoded by the cDNA clone contained in ATCC No. 203518deposited on Dec. 10, 1998; (d) a nucleotide sequence encoding apolypeptide comprising the Neutrokine-alphaSV transmembrane domain(predicted to constitute amino acid residues from about 47 to about 72in FIGS. 5A and 5B (SEQ ID NO:19) or as encoded by the cDNA clonecontained in ATCC No. 203518 deposited on Dec. 10, 1998; (e) anucleotide sequence encoding a soluble Neutrokine-alphaSV polypeptidehaving the extracellular and intracellular domains but lacking thetransmembrane domain; and (f) a nucleotide sequence complementary to anyof the nucleotide sequences in (a), (b), (c), (d), or (e) above.

Further embodiments of the invention include isolated nucleic acidmolecules that comprise, or alternatively consist of, a polynucleotidehaving a nucleotide sequence at least 80%, 85% or 90% identical, andmore preferably at least 95%, 96%, 97%, 98% or 99% identical, to any ofthe nucleotide sequences in (a), (b), (c), (d), (e) or (f) above, or apolynucleotide which hybridizes under stringent hybridization conditionsto a polynucleotide in (a), (b), (c), (d), (e) or (f) above. Thispolynucleotide which hybridizes does not hybridize under stringenthybridization conditions to a polynucleotide having a nucleotidesequence consisting of only A residues or of only T residues.

In one embodiment, the apparent splice variant of Neutrokine-alphacomprising, or alternatively consisting of, at least a portion of theamino acid sequence from Gly-142 to Leu-266 as shown in FIGS. 5A and 5B(SEQ ID NO:19) or amino acid sequence encoded by the cDNA clone HDPMC52deposited on Dec. 10, 1998 and assigned ATCC Deposit No. 203518.

In additional embodiments, the nucleic acid molecules of the inventioncomprise, or alternatively consist of, a polynucleotide which encodesthe amino acid sequence of an epitope-bearing portion of aNeutrokine-alpha or Neutrokine-alphaSV polypeptide having an amino acidsequence in (a), (b), (c), (d), (e), (f) or (g) above. A further nucleicacid embodiment of the invention relates to an isolated nucleic acidmolecule comprising, or alternatively consisting of, a polynucleotidewhich encodes the amino acid sequence of a Neutrokine-alpha orNeutrokine-alphaSV polypeptide having an amino acid sequence whichcontains at least one amino acid addition, substitution, and/or deletionbut not more than 50 amino acid additions, substitutions and/ordeletions, even more preferably, not more than 40 amino acid additions,substitutions, and/or deletions, still more preferably, not more than 30amino acid additions, substitutions, and/or deletions, and still evenmore preferably, not more than 20 amino acid additions, substitutions,and/or deletions. Of course, in order of ever-increasing preference, itis highly preferable for a polynucleotide which encodes the amino acidsequence of a Neutrokine-alpha or Neutrokine-alphaSV polypeptide to havean amino acid sequence which contains not more than 10, 9, 8, 7, 6, 5,4, 3, 2 or 1 or 1-100, 1-50, 1-25, 1-20, 1-15, 1-10, or 1-5 amino acidadditions, substitutions and/or deletions. Conservative substitutionsare preferable.

The present invention also relates to recombinant vectors, which includethe isolated nucleic acid molecules of the present invention, and tohost cells containing the recombinant vectors, as well as to methods ofmaking such vectors and host cells and for using them for production ofNeutrokine-alpha polypeptides by recombinant techniques.

In accordance with a further embodiment of the present invention, thereis provided a process for producing such polypeptides by recombinanttechniques comprising culturing recombinant prokaryotic and/oreukaryotic host cells, containing a Neutrokine-alpha orNeutrokine-alphaSV nucleic acid sequence of the invention, underconditions promoting expression of said polypeptide and subsequentrecovery of said polypeptide.

The invention further provides an isolated Neutrokine-alpha polypeptidecomprising, or alternatively consisting of, an amino acid sequenceselected from the group consisting of: (a) the amino acid sequence ofthe full-length Neutrokine-alpha polypeptide having the complete aminoacid sequence shown in FIGS. 1A and 1B (i.e., positions 1-285 of SEQ IDNO:2) or as encoded by the cDNA plasmid contained in the deposit havingATCC accession number 97768; (b) the amino acid sequence of thefull-length Neutrokine-alpha polypeptide having the complete amino acidsequence shown in SEQ ID NO:2 excepting the N-terminal methionine (i.e.,positions 2 to 285 of SEQ ID NO:2); (c) a fragment of the polypeptide of(b) having Neutrokine-alpha functional activity (e.g., biologicalactivity); (d) the amino acid sequence of the predicted extracellulardomain of the Neutrokine-alpha polypeptide having the amino acidsequence at positions 73 to 285 in FIGS. 1A and 1B (SEQ ID NO:2) or asencoded by the cDNA plasmid contained in the deposit having ATCCaccession number 97768; (e) a nucleotide sequence encoding theNeutrokine-alpha polypeptide having the amino acid sequence at positions134-285 in FIGS. 1A and 1B (SEQ ID NO:2); (f) the amino acid sequence ofthe Neutrokine-alpha intracellular domain (predicted to constitute aminoacid residues from about 1 to about 46 in FIGS. 1A and 1B (SEQ ID NO:2))or as encoded by the cDNA plasmid contained in the deposit having ATCCaccession number 97768; (g) the amino acid sequence of theNeutrokine-alpha transmembrane domain (predicted to constitute aminoacid residues from about 47 to about 72 in FIGS. 1A and 1B (SEQ IDNO:2)) or as encoded by the cDNA plasmid contained in the deposit havingATCC accession number 97768; (h) the amino acid sequence of the solubleNeutrokine-alpha polypeptide having the extracellular and intracellulardomains but lacking the transmembrane domain, wherein each of thesedomains is defined above; and (i) fragments of the polypeptide of (a),(b), (c), (d), (e), (f), (g) or (h). The polypeptides of the presentinvention also include polypeptides having an amino acid sequence atleast 80% identical, more preferably at least 85% or 90% identical, andstill more preferably 95%, 96%, 97%, 98% or 99% identical to thosedescribed in (a), (b), (c), (d), (e) (f), (g), (h) or (i) above, as wellas polypeptides having an amino acid sequence with at least 80%, 85%, or90% similarity, and more preferably at least 95% similarity, to thoseabove. Additional embodiments of the invention relates to polypeptideswhich comprise, or alternatively consist of, the amino acid sequence ofan epitope-bearing portion of a Neutrokine-alpha polypeptide having anamino acid sequence described in (a), (b), (c), (d), (e), (f), (g), (h)or (i) above. Polypeptides having the amino acid sequence of anepitope-bearing portion of a Neutrokine-alpha polypeptide of theinvention include portions of such polypeptides with at least 4, atleast 5, at least 6, at least 7, at least 8, and preferably at least 9,at least 10, at least 11, at least 12, at least 13, at least 14, atleast 15, at least 20, at least 25, at least 30, at least 40, at least50, and more preferably at least about 30 amino acids to about 50 aminoacids, although epitope-bearing polypeptides of any length up to andincluding the entire amino acid sequence of a polypeptide of theinvention described above also are included in the invention.

Highly preferred embodiments of the invention are directed to nucleicacid molecules comprising, or alternatively consisting of apolynucleotide having a nucleotide sequence at least 80%, 85%, 90%identical and more preferably at least 95%, 96%, 97%, 98%, 99% or 100%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). Preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 90%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). More preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 95%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). More preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 96%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2).

Additionally, more preferred embodiments of the invention are directedto nucleic acid molecules comprising, or alternatively consisting of apolynucleotide having a nucleotide sequence at least 97% to apolynucleotide sequence encoding the Neutrokine-alpha polypeptide havingthe amino acid sequence at positions 134-285 in FIGS. 1A and 1B (SEQ IDNO:2). Additionally, more preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 98%to a polynucleotide sequence encoding the Neutrokine-alpha polypeptidehaving the amino acid sequence at positions 134-285 in FIGS. 1A and 1B(SEQ ID NO:2). Additionally, more preferred embodiments of the inventionare directed to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 99%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2).

The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these polynucleotides and nucleic acid molecules are alsoencompassed by the invention.

The invention further provides an isolated Neutrokine-alphaSVpolypeptide comprising, or alternatively consisting of, an amino acidsequence selected from the group consisting of: (a) the amino acidsequence of the full-length Neutrokine-alphaSV polypeptide having thecomplete amino acid sequence shown in FIGS. 5A and 5B (i.e., positions1-266 of SEQ ID NO:19) or as encoded by the cDNA clone contained in ATCCNo. 203518 deposited on Dec. 10, 1998; (b) the amino acid sequence ofthe full-length Neutrokine-alphaSV polypeptide having the complete aminoacid sequence shown in SEQ ID NO:19 excepting the N-terminal methionine(i.e., positions 2 to 266 of SEQ ID NO:19); (c) the amino acid sequenceof the predicted extracellular domain of the Neutrokine-alphaSVpolypeptide having the amino acid sequence at positions 73 to 266 inFIGS. 5A and 5B (SEQ ID NO:19) or as encoded by the cDNA clone containedin ATCC No. 203518 deposited on Dec. 10, 1998; (d) the amino acidsequence of the Neutrokine-alphaSV intracellular domain (predicted toconstitute amino acid residues from about 1 to about 46 in FIGS. 5A and5B (SEQ ID NO:19)) or as encoded by the cDNA clone contained in ATCC No.203518 deposited on Dec. 10, 1998; (e) the amino acid sequence of theNeutrokine-alphaSV transmembrane domain (predicted to constitute aminoacid residues from about 47 to about 72 in FIGS. 5A and 5B (SEQ IDNO:19)) or as encoded by the cDNA clone contained in ATCC No. 203518deposited on Dec. 10, 1998; (f) the amino acid sequence of the solubleNeutrokine-alphaSV polypeptide having the extracellular andintracellular domains but lacking the transmembrane domain, wherein eachof these domains is defined above; and (g) fragments of the polypeptideof (a), (b), (c), (d), (e), or (f). The polypeptides of the presentinvention also include polypeptides having an amino acid sequence atleast 80% identical, more preferably at least 85% or 90% identical, andstill more preferably 95%, 96%, 97%, 98% or 99% identical to thosedescribed in (a), (b), (c), (d), (e) (f), or (g) above, as well aspolypeptides having an amino acid sequence with at least 80%, 85%, or90% similarity, and more preferably at least 95% similarity, to thoseabove. Additional embodiments of the invention relates to polypeptideswhich comprise, or alternatively consist of, the amino acid sequence ofan epitope-bearing portion of a Neutrokine-alphaSV polypeptide having anamino acid sequence described in (a), (b), (c), (d), (e), (f), or (g)above. Peptides or polypeptides having the amino acid sequence of anepitope-bearing portion of a Neutrokine-alphaSV polypeptide of theinvention include portions of such polypeptides with at least 4, atleast 5, at least 6, at least 7, at least 8, and preferably at least 9,at least 10, at least 11, at least 12, at least 13, at least 14, atleast 15, at least 20, at least 25, at least 30, at least 40, at least50, and more preferably at least about 30 amino acids to about 50 aminoacids, although epitope-bearing polypeptides of any length up to andincluding the entire amino acid sequence of a polypeptide of theinvention described above also are included in the invention.

Certain non-exclusive embodiments of the invention relate to apolypeptide which has the amino acid sequence of an epitope-bearingportion of a Neutrokine-alpha or Neutrokine-alphaSV polypeptide havingan amino acid sequence described in (a), (b), (c), (d), (e), (f), (g),(h) or (i) above. In other embodiments, the invention provides anisolated antibody that binds specifically (i.e., uniquely) to aNeutrokine-alpha or Neutrokine-alphaSV polypeptide having an amino acidsequence described in (a), (b), (c), (d), (e), (f), (g), (h) or (i)above.

The invention further provides methods for isolating antibodies thatbind specifically (i.e., uniquely) to a Neutrokine-alpha orNeutrokine-alphaSV polypeptide having an amino acid sequence asdescribed herein. Such antibodies are useful diagnostically ortherapeutically as described below.

The invention also provides for pharmaceutical compositions comprisingsoluble Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides,particularly human Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides, and/or anti-Neutrokine-alpha antibodies and/oranti-Neutrokine-alphaSV antibodies which may be employed, for instance,to treat, prevent, prognose and/or diagnose tumor and tumor metastasis,infections by bacteria, viruses and other parasites, immunodeficiencies,inflammatory diseases, lymphadenopathy, autoimmune diseases, graftversus host disease, stimulate peripheral tolerance, destroy sometransformed cell lines, mediate cell activation, survival andproliferation, to mediate immune regulation and inflammatory responses,and to enhance or inhibit immune responses.

In certain embodiments, soluble Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention, or agonists thereof,are administered, to treat, prevent, prognose and/or diagnose animmunodeficiency (e.g., severe combined immunodeficiency (SCID)-Xlinked, SCID-autosomal, adenosine deaminase deficiency (ADA deficiency),X-linked agammaglobulinemia (XLA), Bruton's disease, congenitalagammaglobulinemia, X-linked infantile agammaglobulinemia, acquiredagammaglobulinemia, adult onset agammaglobulinemia, late-onsetagammaglobulinemia, dysgammaglobulinemia, hypogammaglobulinemia,transient hypogammaglobulinemia of infancy, unspecifiedhypogammaglobulinemia, agammaglobulinemia, common variableimmunodeficiency (CVID) (acquired), Wiskott-Aldrich Syndrome (WAS),X-linked immunodeficiency with hyper IgM, non X-linked immunodeficiencywith hyper IgM, selective IgA deficiency, IgG subclass deficiency (withor without IgA deficiency), antibody deficiency with normal or elevatedIgs, immunodeficiency with thymoma, Ig heavy chain deletions, kappachain deficiency, B cell lymphoproliferative disorder (BLPD), selectiveIgM immunodeficiency, recessive agammaglobulinemia (Swiss type),reticular dysgenesis, neonatal neutropenia, severe congenitalleukopenia, thymic alymphoplasia-aplasia or dysplasia withimmunodeficiency, ataxia-telangiectasia, short limbed dwarfism, X-linkedlymphoproliferative syndrome (XLP), Nezelof syndrome-combinedimmunodeficiency with Igs, purine nucleoside phosphorylase deficiency(PNP), MHC Class II deficiency (Bare Lymphocyte Syndrome) and severecombined immunodeficiency.) or conditions associated with animmunodeficiency.

In a specific embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides or polynucleotides of the invention, or agonists thereof,are administered to treat, prevent, prognose and/or diagnose commonvariable immunodeficiency.

In a specific embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides or polynucleotides of the invention, or agonists thereof,are administered to treat, prevent, prognose and/or diagnose X-linkedagammaglobulinemia.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, prognose and/ordiagnose severe combined immunodeficiency (SCID).

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, prognose and/ordiagnose Wiskott-Aldrich syndrome.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, prognose and/ordiagnose X-linked Ig deficiency with hyper IgM.

In another embodiment, Neutrokine-alpha antagonists and/orNeutrokine-alphaSV antagonists (e.g., an anti-Neutrokine-alphaantibody), are administered to treat, prevent, prognose and/or diagnosean autoimmune disease (e.g., rheumatoid arthritis, systemic lupuserythematosus, idiopathic thrombocytopenia purpura, autoimmune hemolyticanemia, autoimmune neonatal thrombocytopenia, autoimmunocytopenia,hemolytic anemia, antiphospholipid syndrome, dermatitis, allergicencephalomyelitis, myocarditis, relapsing polychondritis, rheumaticheart disease, glomerulonephritis (e.g., IgA nephropathy), MultipleSclerosis, Neuritis, Uveitis Ophthalmia, Polyendocrinopathies, Purpura(e.g., Henloch-Scoenlein purpura), Reiter's Disease, Stiff-Man Syndrome,Autoimmune Pulmonary Inflammation, Guillain-Barre Syndrome, insulindependent diabetes mellitus, and autoimmune inflammatory eye, autoimmunethyroiditis, hypothyroidism (i.e., Hashimoto's thyroiditis,Goodpasture's syndrome, Pemphigus, Receptor autoimmunities such as, forexample, (a) Graves' Disease, (b) Myasthenia Gravis, and (c) insulinresistance, autoimmune hemolytic anemia, autoimmune thrombocytopenicpurpura, schleroderma with anti-collagen antibodies, mixed connectivetissue disease, polymyositis/dermatomyositis, pernicious anemia,idiopathic Addison's disease, infertility, glomerulonephritis such asprimary glomerulonephritis and IgA nephropathy, bullous pemphigoid,Sjogren's syndrome, diabetes mellitus, and adrenergic drug resistance(including adrenergic drug resistance with asthma or cystic fibrosis),chronic active hepatitis, primary biliary cirrhosis, other endocrinegland failure, vitiligo, vasculitis, post-MI, cardiotomy syndrome,urticaria, atopic dermatitis, asthma, inflammatory myopathies, and otherinflammatory, granulomatous, degenerative, and atrophic disorders) orconditions associated with an autoimmune disease. In a specificpreferred embodiment, rheumatoid arthritis is treated, prevented,prognosed and/or diagnosed using anti-Neutrokine-alpha antibodies and/oranti-Neutrokine-alphaSV antibodies and/or other antagonist of theinvention. In another specific preferred embodiment, systemic lupuserythemosus is treated, prevented, prognosed, and/or diagnosed usinganti-Neutrokine-alpha antibodies and/or anti-Neutrokine-alphaSV and/orother antagonist of the invention. In another specific preferredembodiment, idiopathic thrombocytopenia purpura is treated, prevented,prognosed, and/or diagnosed using anti-Neutrokine-alpha antibodiesand/or anti-Neutrokine-alphaSV and/or other antagonist of the invention.In another specific preferred embodiment IgA nephropathy is treated,prevented, prognosed and/or diagnosed using anti-Neutrokine-alphaantibodies and/or anti-Neutrokine-alphaSV and/or other antagonist of theinvention. In a preferred embodiment, the autoimmune diseases anddisorders and/or conditions associated with the diseases and disordersrecited above are treated, prevented, prognosed and/or diagnosed usinganti-Neutrokine-alpha antibodies and/or anti-Neutrokine-alphaSVantibodies.

The invention further provides compositions comprising aNeutrokine-alpha or Neutrokine-alphaSV polynucleotide, aNeutrokine-alpha or Neutrokine-alphaSV polypeptide, and/or ananti-Neutrokine-alpha antibody or anti-Neutrokine-alphaSV antibody, foradministration to cells in vitro, to cells ex vivo, and to cells invivo, or to a multicellular organism. In preferred embodiments, thecompositions of the invention comprise a Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotide for expression of a Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide in a host organism for treatmentof disease. In a most preferred embodiment, the compositions of theinvention comprise a Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotide for expression of a Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide in a host organism for treatment of animmunodeficiency and/or conditions associated with an immunodeficiency.Particularly preferred in this regard is expression in a human patientfor treatment of a dysfunction associated with aberrant endogenousactivity of a Neutrokine-alpha or Neutrokine-alphaSV gene (e.g.,expression to enhance the normal B-cell function by expanding B-cellnumbers or increasing B cell lifespan).

The present invention also provides a screening method for identifyingcompounds capable of enhancing or inhibiting a cellular response inducedby Neutrokine-alpha and/or Neutrokine-alphaSV which involves contactingcells which express Neutrokine-alpha and/or Neutrokine-alphaSV with thecandidate compound, assaying a cellular response, and comparing thecellular response to a standard cellular response, the standard beingassayed when contact is made in absence of the candidate compound;whereby, an increased cellular response over the standard indicates thatthe compound is an agonist and a decreased cellular response over thestandard indicates that the compound is an antagonist.

In another embodiment, a method for identifying Neutrokine-alpha and/orNeutrokine-alphaSV receptors is provided, as well as a screening assayfor agonists and antagonists using such receptors. This assay involvesdetermining the effect a candidate compound has on Neutrokine-alphaand/or Neutrokine-alphaSV binding to the Neutrokine-alpha and/orNeutrokine-alphaSV receptor. In particular, the method involvescontacting a Neutrokine-alpha and/or Neutrokine-alphaSV receptor with aNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide of the inventionand a candidate compound and determining whether Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide binding to the Neutrokine-alpha and/orNeutrokine-alphaSV receptor is increased or decreased due to thepresence of the candidate compound. The antagonists may be employed toprevent septic shock, inflammation, cerebral malaria, activation of theHIV virus, graft-host rejection, bone resorption, rheumatoid arthritis,cachexia (wasting or malnutrition), immune system function, lymphoma,and autoimmune disorders (e.g., rheumatoid arthritis and systemic lupuserythematosus).

The present inventors have discovered that Neutrokine-alpha is expressednot only in cells of monocytic lineage, but also in kidney, lung,peripheral leukocyte, bone marrow, T cell lymphoma, B cell lymphoma,activated T cells, stomach cancer, smooth muscle, macrophages, and cordblood tissue. The present inventors have further discovered thatNeutrokine-alphaSV appears to be expressed highly only in primarydendritic cells. For a number of disorders of these tissues and cells,such as tumor and tumor metastasis, infection of bacteria, viruses andother parasites, immunodeficiencies (e.g., chronic variableimmunodeficiency), septic shock, inflammation, cerebral malaria,activation of the HIV virus, graft-host rejection, bone resorption,rheumatoid arthritis, autoimmune diseases (e.g., rheumatoid arthritisand systemic lupus erythematosus) and cachexia (wasting ormalnutrition). It is believed that significantly higher or lower levelsof Neutrokine-alpha and/or Neutrokine-alphaSV gene expression can bedetected in certain tissues (e.g., bone marrow) or bodily fluids (e.g.,serum, plasma, urine, synovial fluid or spinal fluid) taken from anindividual having such a disorder, relative to a “standard”Neutrokine-alpha and/or Neutrokine-alphaSV gene expression level, i.e.,the Neutrokine-alpha and/or Neutrokine-alphaSV expression level intissue or bodily fluids from an individual not having the disorder.Thus, the invention provides a diagnostic method useful during diagnosisof a disorder, which involves: (a) assaying Neutrokine-alpha and/orNeutrokine-alphaSV gene expression level in cells or body fluid of anindividual; (b) comparing the Neutrokine-alpha and/or Neutrokine-alphaSVgene expression level with a standard Neutrokine-alpha and/orNeutrokine-alphaSV gene expression level, whereby an increase ordecrease in the assayed Neutrokine-alpha and/or Neutrokine-alphaSV geneexpression level compared to the standard expression level is indicativeof a disorder.

An additional embodiment of the invention is related to a method fortreating an individual in need of an increased or constitutive level ofNeutrokine-alpha and/or Neutrokine-alphaSV activity in the bodycomprising administering to such an individual a composition comprisinga therapeutically effective amount of an isolated Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide of the invention or an agonistthereof.

A still further embodiment of the invention is related to a method fortreating an individual in need of a decreased level of Neutrokine-alphaand/or Neutrokine-alphaSV activity in the body comprising, administeringto such an individual a composition comprising a therapeuticallyeffective amount of an Neutrokine-alpha and/or Neutrokine-alphaSVantagonist. Preferred antagonists for use in the present invention areNeutrokine-alpha-specific and/or Neutrokine-alphaSV-specific antibodies.

BRIEF DESCRIPTION OF THE FIGURES

The following drawings are illustrative of embodiments of the inventionand are not meant to limit the scope of the invention as encompassed bythe claims.

FIGS. 1A and 1B show the nucleotide (SEQ ID NO:1) and deduced amino acid(SEQ ID NO:2) sequences of Neutrokine-alpha. Amino acids 1 to 46represent the predicted intracellular domain, amino acids 47 to 72 thepredicted transmembrane domain (the double-underlined sequence), andamino acids 73 to 285, the predicted extracellular domain (the remainingsequence). Potential asparagine-linked glycosylation sites are marked inFIGS. 1A and 1B with a bolded asparagine symbol (N) in theNeutrokine-alpha amino acid sequence and a bolded pound sign (#) abovethe first nucleotide encoding that asparagine residue in theNeutrokine-alpha nucleotide sequence. Potential N-linked glycosylationsequences are found at the following locations in the Neutrokine-alphaamino acid sequence: N-124 through Q-127 (N-124, S-125, S-126, Q-127)and N-242 through C-245 (N-242, N-243, S-244, C-245).

Regions of high identity between Neutrokine-alpha, Neutrokine-alphaSV,TNF-alpha, TNF-beta, LT-beta, and the closely related Fas Ligand (analignment of these sequences is presented in FIGS. 2A, 2B, 2C, and 2D)are underlined in FIGS. 1A and 1B. These regions are not limiting andare labeled as Conserved Domain (CD)-I, CD-II, CD-III, CD-IV, CD-V,CD-VI, CD-VII, CD-VIII, CD-IX, CD-X, and CD-XI in FIGS. 1A and 1B.

FIGS. 2A, 2B, 2C, and 2D show the regions of identity between the aminoacid sequences of Neutrokine-alpha (SEQ ID NO:2) and Neutrokine-alphaSV(SEQ ID NO:19), and TNF-alpha (“TNFalpha” in FIGS. 2A, 2B, 2C, and 2D;GenBank No. Z15026; SEQ ID NO:3), TNF-beta (“TNFbeta” in FIGS. 2A, 2B,2C, and 2D; GenBank No. Z15026; SEQ ID NO:4), Lymphotoxin-beta (“LTbeta”in FIGS. 2A, 2B, 2C, and 2D; GenBank No. L11016; SEQ ID NO:5), and FASligand (“FASL” in FIGS. 2A, 2B, 2C, and 2D; GenBank No. U11821; SEQ IDNO:6), determined by the “MegAlign” routine which is part of thecomputer program called “DNA*STAR.” Residues that match the consensusare shaded.

FIG. 3 shows an analysis of the Neutrokine-alpha amino acid sequence.Alpha, beta, turn and coil regions; hydrophilicity and hydrophobicity;amphipathic regions; flexible regions; antigenic index and surfaceprobability are shown, as predicted for the amino acid sequence of SEQID NO:2 using the default parameters of the recited computer programs.In the “Antigenic Index—Jameson-Wolf” graph, the indicate location ofthe highly antigenic regions of Neutrokine-alpha i.e., regions fromwhich epitope-bearing peptides of the invention may be obtained.Antigenic polypeptides include from about Phe-115 to about Leu-147, fromabout Ile-150 to about Tyr-163, from about Ser-171 to about Phe-194,from about Glu-223 to about Tyr-246, and from about Ser-271 to aboutPhe-278, of the amino acid sequence of SEQ ID NO:2.

The data presented in FIG. 3 are also represented in tabular form inTable I. The columns are labeled with the headings “Res”, “Position”,and Roman Numerals I-XIV. The column headings refer to the followingfeatures of the amino acid sequence presented in FIG. 3, and Table I:“Res”: amino acid residue of SEQ ID NO:2 and FIGS. 1A and 1B;“Position”: position of the corresponding residue within SEQ ID NO:2 andFIGS. 1A and 1B; I: Alpha, Regions—Garnier-Robson; II: Alpha,Regions—Chou-Fasman; III: Beta, Regions—Garnier-Robson; IV: Beta,Regions—Chou-Fasman; V: Turn, Regions—Garnier-Robson; VI: Turn,Regions—Chou-Fasman; VII: Coil, Regions—Garnier-Robson; VIII:Hydrophilicity Plot—Kyte-Doolittle; IX: Hydrophobicity Plot—Hopp-Woods;X: Alpha, Amphipathic Regions—Eisenberg; XI: Beta, AmphipathicRegions—Eisenberg; XII: Flexible Regions—Karplus-Schulz; XIII: AntigenicIndex—Jameson-Wolf; and XIV: Surface Probability Plot—Emini.

FIGS. 4A, 4B, and 4C show the alignment of the Neutrokine-alphanucleotide sequence (SEQ ID NO:1) determined from the human cDNA clone(HNEDU15) deposited in ATCC No. 97768 with related human cDNA clones ofthe invention which have been designated HSOAD55 (SEQ ID NO:7), HSLAH84(SEQ ID NO:8) and HLTBM08 (SEQ ID NO:9).

FIGS. 5A and 5B show the nucleotide (SEQ ID NO:18) and deduced aminoacid (SEQ ID NO:19) sequences of the Neutrokine-alphaSV protein. Aminoacids 1 to 46 represent the predicted intracellular domain, amino acids47 to 72 the predicted transmembrane domain (the double-underlinedsequence), and amino acids 73 to 266, the predicted extracellular domain(the remaining sequence). Potential asparagine-linked glycosylationsites are marked in FIGS. 5A and 5B with a bolded asparagine symbol (N)in the Neutrokine-alphaSV amino acid sequence and a bolded pound sign(#) above the first nucleotide encoding that asparagine residue in theNeutrokine-alphaSV nucleotide sequence. Potential N-linked glycosylationsequences are found at the following locations in the Neutrokine-alphaSVamino acid sequence: N-124 through Q-127 (N-124, S-125, S-126, Q-127)and N-223 through C-226 (N-223, N-224, S-225, C-226). Antigenicpolypeptides include from about Pro-32 to about Leu-47, from aboutGlu-116 to about Ser-143, from about Phe-153 to about Tyr-173, fromabout Pro-218 to about Tyr-227, from about Ala-232 to about Gln-241;from about Ile-244 to about Ala-249; and from about Ser-252 to aboutVal-257 of the amino acid sequence of SEQ ID NO:19.

Regions of high identity between Neutrokine-alpha, Neutrokine-alphaSV,TNF-alpha, TNF-beta, LT-beta, and the closely related Fas Ligand (analignment of these sequences is presented in FIGS. 2A, 2B, 2C, and 2D)are underlined in FIGS. 1A and 1B. These conserved regions (ofNeutrokine-alpha and Neutrokine-alphaSV) are labeled as Conserved Domain(CD)-I, CD-II, CD-III, CD-V, CD-VI, CD-VII, CD-VIII, CD-IX, CD-X, andCD-XI in FIGS. 5A and 5B. Neutrokine-alphaSV does not contain thesequence of CD-IV described in the legend of FIGS. 1A and 1B.

An additional alignment of the Neutrokine-alpha polypeptide sequence(SEQ ID NO:2) with APRIL, TNF alpha, and LT alpha is presented in FIGS.7A-1 and 7A-2. In FIGS. 7A-1 and 7A-2, beta sheet regions are indicatedas described below in the legend to FIGS. 7A-1 and 7A-2.

FIG. 6 shows an analysis of the Neutrokine-alphaSV amino acid sequence.Alpha, beta, turn and coil regions; hydrophilicity and hydrophobicity;amphipathic regions; flexible regions; antigenic index and surfaceprobability are shown, as predicted for the amino acid sequence of SEQID NO:19 using the default parameters of the recited computer programs.The location of the highly antigenic regions of the Neutrokine-alphaprotein, i.e., regions from which epitope-bearing peptides of theinvention may be obtained is indicated in the “AntigenicIndex—Jameson-Wolf” graph. Antigenic polypeptides include, but are notlimited to, a polypeptide comprising amino acid residues from aboutPro-32 to about Leu-47, from about Glu-116 to about Ser-143, from aboutPhe-153 to about Tyr-173, from about Pro-218 to about Tyr-227, fromabout Ser-252 to about Thr-258, from about Ala-232 to about Gln-241;from about Ile-244 to about Ala-249; and from about Ser-252 to aboutVal-257, of the amino acid sequence of SEQ ID NO:19.

The data shown in FIG. 6 can be easily represented in tabular formatsimilar to the data shown in Table I. Such a tabular representation ofthe exact data disclosed in FIG. 6 can be generated using the MegAligncomponent of the DNA*STAR computer sequence analysis package set ondefault parameters. This is the identical program that was used togenerate FIGS. 3 and 6 of the present application.

FIGS. 7A-1 and 7A-2. The amino-acid sequence of Neutrokine-alpha andalignment of its predicted ligand-binding domain with those of APRIL,TNF-alpha, and LT-alpha (specifically, amino acid residues 115-250 ofthe human APRIL polypeptide (SEQ ID NO:20; ATCC Accession No. AF046888),amino acid residues 88-233 of TNF alpha (SEQ ID NO:3; GenBank AccessionNo. Z15026), and LT alpha ((also designated TNF-beta) amino acidresidues 62-205 of SEQ ID NO:4; GenBank Accession No. Z15026)). Thepredicted membrane-spanning region of Neutrokine-alpha is indicated andthe site of cleavage of Neutrokine-alpha is depicted with an arrow.Sequences overlaid with lines (A thru H) represent predictedbeta-pleated sheet regions.

FIG. 7B. Expression of Neutrokine-alpha mRNA. Northern hybridizationanalysis was performed using the Neutrokine-alpha orf as a probe onblots of poly(A)+ RNA (Clontech) from a spectrum of human tissue typesand a selection of cancer cell lines. A 2.6 kb Neutrokine-alpha mRNA wasdetected at high levels in placenta, heart, lung, fetal liver, thymus,and pancreas. The 2.6 kb Neutrokine-alpha mRNA was also detected inHL-60 and K562 cell lines.

FIGS. 8A, 8B, and 8C. Neutrokine-alpha expression increases followingactivation of human monocytes by IFN-gamma. FIGS. 8A and 8B. Flowcytometric analysis of Neutrokine-alpha protein expression on in vitrocultured monocytes. Purified monocytes were cultured for 3 days inpresence or absence of IFN-gamma (100 U/ml). Cells were then stainedwith a Neutrokine-alpha-specific mAb (2E5) (solid lines) or anisotype-matched control (IgG1) (dashed lines). Comparable results wereobtained with monocytes purified from three different donors in threeindependent experiments. FIG. 8C. Neutrokine-alpha-specific TaqManprimers were prepared and used to assess the relative Neutrokine-alphamRNA expression levels in unstimulated and IFN-gamma (100 U/mL) treatedmonocytes. Nucleotide sequences of the TaqMan primers are as follows:(a) Probe: 5′-CCA CCA GCT CCA GGA GAA GGC AAC TC-3′ (SEQ ID NO:24); (b)5′ amplification primer: 5′-ACC GCG GGA CTG AAA ATC T-3′ (SEQ ID NO:25);and (c) 3′ amplification primer: 5′-CAC GCT TAT TTC TGC TGT TCT GA-3′(SEQ ID NO:26).

FIGS. 9A and 9B. Neutrokine-alpha is a potent B lymphocyte stimulator.FIG. 9A. The biological activity of Neutrokine-alpha was assessed in astandard B-lymphocyte co-stimulation assay utilizing Staphylococcusaureus cowan 1 SAC as the priming agent. SAC alone yielded backgroundcounts of 1427+/−316. Values are reported as mean+/−standard deviationof triplicate wells. Similar results were obtained using recombinantNeutrokine-alpha purified from stable CHO transfectants and transientlytransfected HEK 293T cells. FIG. 9B. Proliferation of tonsillar B cellswith Neutrokine-alpha and co-stimulation with anti-IgM. The bioassay wasperformed as described for SAC with the exception that individual wellswere pre-coated with goat anti-human IgM antibody at 10 micrograms/mL inPBS.

FIGS. 10A, 10B, 10C, 10D, 10E, 10F and 10G. Neutrokine-alpha receptorexpression among normal human peripheral blood mononuclear cells andtumor cell lines. FIGS. 10A, 10B, 10C, 10D and 10E. Human peripheralblood nucleated cells were obtained from normal volunteers and isolatedby density gradient centrifugation. Cells were stained with biotinylatedNeutrokine-alpha followed by PE-conjugated streptavidin and FITC orPerCP coupled mAbs specific for CD3, CD20, CD14, CD56, and CD66b. Cellswere analyzed on a Becton Dickinson FACScan using the CellQuestsoftware. Data represent one of four independent experiments. FIGS. 10Fand 10G. Neutrokine-alpha binding to histiocytic cell line U-937 and themyeloma line IM-9.

FIGS. 11A, 11B, 11C, 11D, 11E and 11F. In vivo effects ofNeutrokine-alpha administration in BALB/cAnNCR mice. FIG. 11A.Formalin-fixed spleens were paraffin embedded and 5 micrometer sectionsstained with hematoxylin and eosin (upper panels). The lower panels aresections taken from the same animals stained with anti-CD45R(B220) mAband developed with horseradish-peroxidase coupled rabbit anti-rat Ig(mouse adsorbed) and the substrate diaminobenzidine tetrahydrochloride(DAB). Slides were counter-stained with Mayer's hematoxylin. CD45R(B220)expressing cells appear brown. FIGS. 11B and 11C. Flow cytometricanalyses of normal (left panel) and Neutrokine-alpha-treated (rightpanel) stained with PE-CD45R(B220) and FITC-ThB (Ly6D). FIGS. 11D, 11E,and 11F. Serum IgM, IgG, and IgA levels in normal and Neutrokine-alphatreated mice.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides isolated nucleic acid moleculescomprising a polynucleotide encoding a Neutrokine-alpha polypeptideshaving the amino acid sequences shown in FIGS. 1A and 1B (SEQ ID NO:2),which was determined by sequencing a cDNA clone. The nucleotide sequenceshown in FIGS. 1A and 1B (SEQ ID NO:1) was obtained by sequencing theHNEDU15 clone, which was deposited on Oct. 22, 1996 at the American TypeCulture Collection, 10801 University Boulevard, Manassas, Va.20110-2209, and assigned ATCC Accession No. 97768. The deposited cloneis contained in the pBluescript SK(−) plasmid (Stratagene, La Jolla,Calif.).

The present invention also provides isolated nucleic acid moleculescomprising a polynucleotide encoding Neutrokine-alphaSV polypeptideshaving the amino acid sequences shown in FIGS. 5A and 5B (SEQ ID NO:19),which was determined by sequencing a cDNA clone. The nucleotide sequenceshown in FIGS. 5A and 5B (SEQ ID NO:18) was obtained by sequencing theHDPMC52 clone, which was deposited on Dec. 10, 1998 at the American TypeCulture Collection, and assigned ATCC Accession No. 203518. Thedeposited clone is contained in the pBluescript SK(−) plasmid(Stratagene, La Jolla, Calif.).

The Neutrokine-alpha and Neutrokine-alpha polypeptides of the presentinvention share sequence homology with the translation products of thehuman mRNAs for TNF-alpha, TNF-beta, LTbeta, Fas ligand, APRIL, andLTalpha. (See, FIGS. 2A, 2B, 2C, 2D, 7A-1 and 7A-2). As noted above,TNF-alpha is thought to be an important cytokine that plays a role incytotoxicity, necrosis, apoptosis, costimulation, proliferation, lymphnode formation, immunoglobulin class switch, differentiation, antiviralactivity, and regulation of adhesion molecules and other cytokines andgrowth factors.

Nucleic Acid Molecules

Unless otherwise indicated, all nucleotide sequences determined bysequencing a DNA molecule herein were determined using an automated DNAsequencer (such as the Model 373 from Applied Biosystems, Inc., FosterCity, Calif.), and all amino acid sequences of polypeptides encoded byDNA molecules determined herein were predicted by translation of a DNAsequence determined as above. Therefore, as is known in the art for anyDNA sequence determined by this automated approach, any nucleotidesequence determined herein may contain some errors. Nucleotide sequencesdetermined by automation are typically at least about 90% identical,more typically at least about 95% to at least about 99.9% identical tothe actual nucleotide sequence of the sequenced DNA molecule. The actualsequence can be more precisely determined by other approaches includingmanual DNA sequencing methods well known in the art. As is also known inthe art, a single insertion or deletion in a determined nucleotidesequence compared to the actual sequence will cause a frame shift intranslation of the nucleotide sequence such that the predicted aminoacid sequence encoded by a determined nucleotide sequence will becompletely different from the amino acid sequence actually encoded bythe sequenced DNA molecule, beginning at the point of such an insertionor deletion.

By “nucleotide sequence” of a nucleic acid molecule or polynucleotide isintended, for a DNA molecule or polynucleotide, a sequence ofdeoxyribonucleotides, and for an RNA molecule or polynucleotide, thecorresponding sequence of ribonucleotides (A, G, C and U), where eachthymidine deoxyribonucleotide (T) in the specified deoxyribonucleotidesequence is replaced by the ribonucleotide uridine (U).

Using the information provided herein, such as the nucleotide sequencein FIGS. 1A and 1B, a nucleic acid molecule of the present inventionencoding a Neutrokine-alpha polypeptide may be obtained using standardcloning and screening procedures, such as those for cloning cDNAs usingmRNA as starting material. Illustrative of the invention, the nucleicacid molecule described in FIGS. 1A and 1B (SEQ ID NO:1) was discoveredin a cDNA library derived from neutrophils. Expressed sequence tagscorresponding to a portion of the Neutrokine-alpha cDNA were also foundin kidney, lung, peripheral leukocyte, bone marrow, T cell lymphoma, Bcell lymphoma, activated T cells, stomach cancer, smooth muscle,macrophages, and cord blood tissue. In addition, using the nucleotideinformation provided in FIGS. 5A and 5B, a nucleic acid molecule of thepresent invention encoding a Neutrokine-alphaSV polypeptide may beobtained using standard cloning and screening procedures, such as thosefor cloning cDNAs using mRNA as starting material. Illustrative of theinvention, the nucleic acid molecule described in FIGS. 5A and 5B (SEQID NO:18) was discovered in a cDNA library derived from primarydendritic cells.

The Neutrokine-alpha plasmid HNEDU15 deposited as ATCC Accession No.97768 contains an open reading frame encoding a protein of about 285amino acid residues, a predicted intracellular domain of about 46 aminoacids (amino acid residues from about 1 to about 46 in FIGS. 1A and 1B(SEQ ID NO:2)), a predicted transmembrane domain of about 26 amino acids(underlined amino acid residues from about 47 to about 72 in FIGS. 1Aand 1B (SEQ ID NO:2)), a predicted extracellular domain of about 213amino acids (amino acid residues from about 73 to about 285 in FIGS. 1Aand 1B (SEQ ID NO:2)); and a deduced molecular weight of about 31 kDa.The Neutrokine-alpha polypeptide shown in FIGS. 1A and 1B (SEQ ID NO:2)is about 20% similar and about 10% identical to human TNF-alpha, whichcan be accessed on GenBank as Accession No. 339764.

The Neutrokine-alphaSV plasmid HDPMC52, deposited as ATCC Accession No.203518, contains a predicted open reading frame encoding a protein ofabout 266 amino acid residues, a predicted intracellular domain of about46 amino acids (amino acid residues from about 1 to about 46 in FIGS. 5Aand 5B (SEQ ID NO:19)), a predicted transmembrane domain of about 26amino acids (underlined amino acid residues from about 47 to about 72 inFIGS. 5A and 5B (SEQ ID NO:19)), a predicted extracellular domain ofabout 194 amino acids (amino acid residues from about 73 to about 266 inFIGS. 5A and 5B (SEQ ID NO:19)); and a deduced molecular weight of about29 kDa. The Neutrokine-alphaSV polypeptide shown in FIGS. 5A and 5B (SEQID NO:19) is about 33.9% similar and about 22.0% identical to humanTNF-alpha which can be accessed on GenBank as Accession No. 339764.

As one of ordinary skill would appreciate, due to the possibilities ofsequencing errors discussed above, the actual complete Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides encoded by the deposited cDNAs,which comprise about 285 and 266 amino acids, respectively, may besomewhat shorter. In particular, the determined Neutrokine-alpha andNeutrokine-alphaSV coding sequences contain a common second methioninecodon which may serve as an alternative start codon for translation ofthe open reading frame, at nucleotide positions 210-212 in FIGS. 1A and1B (SEQ ID NO:1) and at nucleotide positions 64-66 in FIGS. 5A and 5B(SEQ ID NO:18). More generally, the actual open reading frame may beanywhere in the range of ±20 amino acids, more likely in the range of±10 amino acids, of that predicted from either the first or secondmethionine codon from the N-terminus shown in FIGS. 1A and 1B (SEQ IDNO:1) and in FIGS. 5A and 5B (SEQ ID NO:18). It will further beappreciated that, the polypeptide domains described herein have beenpredicted by computer analysis, and accordingly, that depending on theanalytical criteria used for identifying various functional domains, theexact “address” of the extracellular, intracellular and transmembranedomains of the Neutrokine-alpha and Neutrokine-alphaSV polypeptides maydiffer slightly. For example, the exact location of the Neutrokine-alphaand Neutrokine-alphaSV extracellular domains in FIGS. 1A and 1B (SEQ IDNO:2) and FIGS. 5A and 5B (SEQ ID NO:19) may vary slightly (e.g., theaddress may “shift” by about 1 to about 20 residues, more likely about 1to about 5 residues) depending on the criteria used to define thedomain. In this case, the ends of the transmembrane domains and thebeginning of the extracellular domains were predicted on the basis ofthe identification of the hydrophobic amino acid sequence in the aboveindicated positions, as shown in FIGS. 3 and 6 and in Table I. In anyevent, as discussed further below, the invention further providespolypeptides having various residues deleted from the N-terminus and/orC-terminus of the complete polypeptides, including polypeptides lackingone or more amino acids from the N-termini of the extracellular domainsdescribed herein, which constitute soluble forms of the extracellulardomains of the Neutrokine-alpha and Neutrokine-alphaSV polypeptides.

As indicated, nucleic acid molecules and polynucleotides of the presentinvention may be in the form of RNA, such as mRNA, or in the form ofDNA, including, for instance, cDNA and genomic DNA obtained by cloningor produced synthetically. The DNA may be double-stranded orsingle-stranded. Single-stranded DNA or RNA may be the coding strand,also known as the sense strand, or it may be the non-coding strand, alsoreferred to as the anti-sense strand.

By “isolated” nucleic acid molecule(s) is intended a nucleic acidmolecule (DNA or RNA), which has been removed from its nativeenvironment. For example, recombinant DNA molecules contained in avector are considered isolated for the purposes of the presentinvention. Further examples of isolated DNA molecules includerecombinant DNA molecules maintained in heterologous host cells orpurified (partially or substantially) DNA molecules in solution.Isolated RNA molecules include in vivo or in vitro RNA transcripts ofthe DNA molecules of the present invention. However, a nucleic acidcontained in a clone that is a member of a library (e.g., a genomic orcDNA library) that has not been isolated from other members of thelibrary (e.g., in the form of a homogeneous solution containing theclone and other members of the library) or a chromosome isolated orremoved from a cell or a cell lysate (e.g., a “chromosome spread”, as ina karyotype), is not “isolated” for the purposes of this invention. Asdiscussed further herein, isolated nucleic acid molecules according tothe present invention may be produced naturally, recombinantly, orsynthetically.

Isolated nucleic acid molecules of the present invention include DNAmolecules comprising, or alternatively consisting of, an open readingframe (ORF) with an initiation codon at positions 147-149 of thenucleotide sequence shown in FIGS. 1A and 1B (SEQ ID NO:1). In addition,isolated nucleic acid molecules of the invention include DNA moleculeswhich comprise, or alternatively consist of, a sequence substantiallydifferent from those described above, but which due to the degeneracy ofthe genetic code, still encode the Neutrokine-alpha protein. Of course,the genetic code is well known in the art. Thus, it would be routine forone skilled in the art to generate the degenerate variants describedabove. In another embodiment, the invention provides isolated nucleicacid molecules comprising, or alternatively consisting of, a sequenceencoding the Neutrokine-alpha polypeptide having an amino acid sequenceencoded by the cDNA contained in the plasmid having ATCC accessionnumber 97768. Preferably, this nucleic acid molecule comprises, oralternatively consists of a sequence encoding the extracellular domainthe mature or soluble polypeptide sequence of the polypeptide encoded bythe cDNA contained in the plasmid having ATCC accession number 97768.

Isolated nucleic acid molecules of the present invention also includeDNA molecules comprising an open reading frame (ORF) with an initiationcodon at positions 1-3 of the nucleotide sequence shown in FIGS. 5A and5B (SEQ ID NO:18). In addition, isolated nucleic acid molecules of theinvention include DNA molecules which comprise, or alternatively consistof, a sequence substantially different from those described above, butwhich due to the degeneracy of the genetic code, still encodes theNeutrokine-alphaSV polypeptide. Of course, the genetic code is wellknown in the art. Thus, it would be routine for one skilled in the artto generate the degenerate variants described above. In anotherembodiment, the invention provides isolated nucleic acid moleculescomprising, or alternatively consisting of, a sequence encoding theNeutrokine-alphaSV polypeptide having an amino acid encoded by the cDNAcontained in the plasmid having ATCC accession number 203518.Preferably, this nucleic acid molecule comprises, or alternativelyconsists of, a sequence encoding the extracellular domain or the maturesoluble polypeptide sequence of the polypeptide encoded by the cDNAcontained in the plasmid having ATCC accession number 203518.

The invention further provides an isolated nucleic acid moleculecomprising, or alternatively consisting of, the nucleotide sequenceshown in FIGS. 1A and 1B (SEQ ID NO:1) or the nucleotide sequence of theNeutrokine-alpha cDNA contained in the plasmid having ATCC accessionnumber 97768, or a nucleic acid molecule having a sequence complementaryto one of the above sequences. In addition, the invention provides anisolated nucleic acid molecule comprising, or alternatively, consistingof, the nucleotide sequence shown in FIGS. 5A and 5B (SEQ ID NO:18) orthe nucleotide sequence of the Neutrokine-alpha SV cDNA contained in theplasmid having ATCC accession number 203518, or a nucleic acid moleculehaving a sequence complementary to one of the above sequences. Suchisolated molecules, particularly DNA molecules, have uses which include,but are not limited to, as probes for gene mapping by in situhybridization with chromosomes, and for detecting expression of theNeutrokine-alpha and Neutrokine-alphaSV in human tissue, for instance,by Northern or Western blot analysis.

In one embodiment, the polynucleotides of the invention comprise, oralternatively consist of, the sequence shown in SEQ ID NO:22. Thesequence provided as SEQ ID NO:22 was constructed from severaloverlapping mouse EST sequences obtained from GenBank (AI182472,AA422749, AA254047, and AI122485). The EST sequences were aligned togenerate the Neutrokine-alpha-like polynucleotide sequence provided asSEQ ID NO:22. The amino acid sequence resulting from the translation ofSEQ ID NO:22 is provided as SEQ ID NO:23. Fragments, variants, andderivatives of the sequences provided as SEQ ID NO:22 and SEQ ID NO:23are also encompassed by the invention.

In another embodiment, the polynucleotides of the invention comprise, oralternatively consist of, the sequence shown in SEQ ID NO:27, and/or asequence encoding the amino acid sequence disclosed in SEQ ID NO:28,fragments, variants, and derivatives thereof. These polynucleotides arealso encompassed by the invention. For example, certain embodiments ofthe invention are directed to polynucleotides comprising, oralternatively consisting of, a sequence encoding a polypeptide sequencethat is at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%, or 99%identical to amino acids 68-219 of SEQ ID NO:28. The amino acid sequenceresulting from the translation of SEQ ID NO:27 is provided as SEQ IDNO:28. Polypeptides comprising, or alternatively consisting of, theamino acid sequence of SEQ ID NO:28, and fragments, variants, andderivatives of the sequence provided as SEQ ID NO:28 are alsoencompassed by the invention. For example, certain embodiments of theinvention are directed to polypeptides comprising, or alternativelyconsisting of, a polypeptide sequence that is at least 80%, 85%, 90%,92%, 95%, 96%, 97%, 98%, or 99% identical to amino acids 68-219 of SEQID NO:28. A nucleic acid molecule having the sequence provided as SEQ IDNO:27 was obtained by RT-PCR from cynomolgous monkey (i.e., Macaca irus)PBMC using two degenerate primers. Briefly, total RNA was prepared fromcynomolgous monkey PBMC by using Trizol (available from LifeTechnologies, Inc., Rockville, Md.) according to the manufacturer'sprotocol. Then a single stranded cDNA was synthesized from thecynomolgous monkey PBMC preparation using standard methods with anoligo-dT primer. Neutrokine-alpha-specific primers were designed basedon the conserved region between the mouse and human Neutrokine-alphamolecules (SEQ ID NOs:22 and 1, respectively). A cynomolgous monkeyNeutrokine-alpha nucleic acid molecule was then generated by PCR usingthe cDNA template in combination with the following two degenerateoligonucleotide primers. 5′ primer: 5′-TAC CAG ITG GCI GCC ITG CAA G-3′(SEQ ID NO:35) and 3′ primer: 5′-GTI ACA GCA GTT TIA IIG CAC C-3′ (SEQID NO:36). In the sequence of the degenerate primers (SEQ ID NOs:35 and36), “I” represents deoxyinosine or dideoxyinosine.

In another embodiment, the polynucleotides of the invention comprise, oralternatively consist of, the sequence shown in SEQ ID NO:29, and/or asequence encoding the amino acid sequence disclosed in SEQ ID NO:30,fragments, variants, and derivatives thereof. These polynucleotides arealso encompassed by the invention. For example, certain embodiments ofthe invention are directed to polynucleotides comprising, oralternatively consisting of, a sequence encoding a polypeptide sequencethat is at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%, or 99%identical to amino acids 68-219 of SEQ ID NO:30. The amino acid sequenceresulting from the translation of SEQ ID NO:29 is provided as SEQ IDNO:30. Polypeptides comprising, or alternatively consisting of, theamino acid sequence of SEQ ID NO:30, and fragments, variants, andderivatives of the sequences provided as SEQ ID NO:29 and SEQ ID NO:30are also encompassed by the invention. For example, certain embodimentsof the invention are directed to polypeptides comprising, oralternatively consisting of, a polypeptide sequence that is at least80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% identical to amino acids68-219 of SEQ ID NO:30. A nucleic acid molecule having the sequenceprovided as SEQ ID NO:29 was obtained by RT-PCR from rhesus monkey PBMCusing two degenerate primers. Briefly, total RNA was prepared fromrhesus monkey PBMC by using Trizol (available from Life Technologies,Inc., Rockville, Md.) according to the manufacturer's protocol. Then asingle stranded cDNA was synthesized from the rhesus monkey PBMCpreparation using standard methods with an oligo-dT primer.Neutrokine-alpha-specific primers were designed based on the conservedregion between the mouse and human Neutrokine-alpha molecules (SEQ IDNOs:22 and 1, respectively). A rhesus monkey Neutrokine-alpha nucleicacid molecule was then generated by PCR using the cDNA template incombination with the following two degenerate oligonucleotide primers.5′ primer: 5′-TAC CAG ITG GCI GCC ITG CAA G-3′ (SEQ ID NO:35) and 3′primer: 5′-GTI ACA GCA GTT TIA IIG CAC C-3′ (SEQ ID NO:36). In thesequence of the degenerate primers (SEQ ID NOs:35 and 36), “I”represents deoxyinosine or dideoxyinosine.

The invention also provides nucleic acid molecules having nucleotidesequences related to extensive portions of SEQ ID NO:1 and SEQ ID NO:18which have been determined from the following related cDNA clones:HSOAD55 (SEQ ID NO:7), HSLAH84 (SEQ ID NO:8), and HLTBM08 (SEQ ID NO:9).

The present invention is further directed to nucleic acid moleculesencoding portions of the nucleotide sequences described herein, as wellas to fragments of the isolated nucleic acid molecules described herein.In one embodiment, the invention provides a polynucleotide having anucleotide sequence representing the portion of SEQ ID NO:1 whichconsists of the nucleotides at positions 1-1001 of SEQ ID NO:1. Inanother embodiment, the invention provides a polynucleotide having anucleotide sequence representing the portion of SEQ ID NO:18 whichconsists of positions 1-798 of SEQ ID NO:18.

The present invention is further directed to fragments of the nucleicacid molecules (i.e. polynucleotides) described herein. By a fragment ofa nucleic acid molecule having, for example, the nucleotide sequence ofthe cDNA contained in the plasmid having ATCC accession number 97768, anucleotide sequence encoding the polypeptide sequence encoded by thecDNA contained in the plasmid having ATCC accession number 97768, thenucleotide sequence of SEQ ID NO:1, a nucleotide sequence encoding thepolypeptide sequence of SEQ ID NO:2, the nucleotide sequence of the cDNAcontained in the plasmid having ATCC accession number 203518, anucleotide sequence encoding the polypeptide sequence encoded by thecDNA contained in the plasmid having ATCC accession number 203518, thenucleotide sequence of SEQ ID NO:18, a nucleotide sequence encoding thepolypeptide sequence of SEQ ID NO:20, or the complementary strandthereto, is intended fragments at least 15 nt, and more preferably atleast 20 nt or at least 25 nt, still more preferably at least 30 nt, andeven more preferably, at least 40, 50, 100, 150, 200, 250, 300, 325,350, 375, 400, 450, or 500 nt in length. These fragments have numeroususes which include, but are not limited to, diagnostic probes andprimers as discussed herein. Of course, larger fragments, such as thoseof 501-1500 nt in length are also useful according to the presentinvention as are fragments corresponding to most, if not all, of thenucleotide sequences of the cDNA contained in the plasmid having ATCCaccession number 97768, the nucleotide sequence of SEQ ID NO:1, thenucleotide sequences of the cDNA contained in the plasmid having ATCCaccession number 203518, and the nucleotide sequence of SEQ ID NO:18.Preferred nucleic acid fragments of the present invention includenucleic acid molecules encoding polypeptides comprising, oralternatively, consisting of, epitope-bearing portions of theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide as identified inFIGS. 1A and 1B (SEQ ID NO:2) and in FIGS. 5A and 5B (SEQ ID NO:19),respectively, and described in more detail below. Polypeptides encodedby these polynucleotide fragments are also encompassed by the invention.

Also by a fragment of a nucleic acid molecule having, for example, thenucleotide sequence of SEQ ID NO:21, the nucleotide sequence of SEQ IDNO:22, the nucleotide sequence of SEQ ID NO:27, the nucleotide sequenceof SEQ ID NO:29, a nucleotide sequence encoding the polypeptide sequenceof SEQ ID NO:23, a nucleotide sequence encoding the polypeptide sequenceof SEQ ID NO:28, a nucleotide sequence encoding the polypeptide sequenceof SEQ ID NO:30, or the complementary strands thereof, is intendedfragments at least 15 nt, and more preferably at least 20 nt or at least25 nt, still more preferably at least 30 nt, and even more preferably,at least 40, 50, 100, 150, 200, 250, 300, 325, 350, 375, 400, 450, or500 nt in length. These fragments have numerous uses which include, butare not limited to, diagnostic probes and primers as discussed herein.Of course, larger fragments, such as those of 501-1500 nt in length arealso useful according to the present invention as are fragmentscorresponding to most, if not all, of the nucleotide sequence of SEQ IDNO:21, the nucleotide sequence of SEQ ID NO:22, the nucleotide sequenceof SEQ ID NO:27, the nucleotide sequence of SEQ ID NO:29, a nucleotidesequence encoding the polypeptide sequence of SEQ ID NO:23, a nucleotidesequence encoding the polypeptide sequence of SEQ ID NO:28, a nucleotidesequence encoding the polypeptide sequence of SEQ ID NO:30, or thecomplementary strands thereof. Polypeptides encoded by thesepolynucleotide fragments are also encompassed by the invention.

Representative examples of Neutrokine-alpha polynucleotide fragments ofthe invention include, for example, fragments that comprise, oralternatively, consist of, a sequence from about nucleotide 1 to 50, 51to 100, 101 to 146, 147 to 200, 201 to 250, 251 to 300, 301 to 350, 351to 400, 401 to 450, 451 to 500, 501 to 550, 551 to 600, 600 to 650, 651to 700, 701 to 750, 751 to 800, 800 to 850, 851 to 900, 901 to 950, 951to 1000, 1001 to 1050, and/or 1051 to 1082, of SEQ ID NO:1, or thecomplementary strand thereto, or the cDNA contained in the plasmidhaving ATCC accession number 97768. In this context “about” includes theparticularly recited ranges, and ranges that are larger or smaller byseveral (5, 4, 3, 2, or 1) nucleotides, at either terminus or at bothtermini.

Representative examples of Neutrokine-alphaSV polynucleotide fragmentsof the invention include, for example, fragments that comprise, oralternatively, consist of, a sequence from about nucleotide 1 to 50, 51to 100, 101 to 150, 151 to 200, 201 to 250, 251 to 300, 301 to 350, 351to 400, 401 to 450, 451 to 500, 501 to 550, 551 to 600, 600 to 650, 651to 700, 701 to 750, 751 to 800, 800 to 850, and/or 851 to 900 of SEQ IDNO:18, or the complementary strand thereto, or the cDNA contained in theplasmid having ATCC accession number 203518. In this context “about”includes the particularly recited ranges, and ranges that are larger orsmaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus orat both termini.

In certain preferred embodiments, polynucleotide of the inventioncomprise, or alternatively, consist of, nucleotide residues 571-627,580-627, 590-627, 600-627, 610-627, 571-620, 580-620, 590-620, 600-620,571-610, 580-610, 590-610, 571-600, 580-600, and/or 571-590 of SEQ IDNO:1.

In certain other preferred embodiments, polynucleotides of the inventioncomprise, or alternatively, consist of nucleotide residues 1-879,25-879, 50-879, 75-879, 100-879, 125-879, 150-879, 175-879, 200-879,225-879, 250-879, 275-879, 300-879, 325-879, 350-879, 375-879, 400-879,425-879, 450-879, 475-879, 500-879, 525-879, 550-879, 575-879, 600-879,625-879, 650-879, 675-879, 700-879, 725-879, 750-879, 775-879, 800-879,825-879, 850-879, 1-850, 25-850, 50-850, 75-850, 100-850, 125-850,150-850, 175-850, 200-850, 225-850, 250-850, 275-850, 300-850, 325-850,350-850, 375-850, 400-850, 425-850, 450-850, 475-850, 500-850, 525-850,550-850, 575-850, 600-850, 625-850, 650-850, 675-850, 700-850, 725-850,750-850, 775-850, 800-850, 825-850, 1-825, 25-825, 50-825, 75-825,100-825, 125-825, 150-825, 175-825, 200-825, 225-825, 250-825, 275-825,300-825, 325-825, 350-825, 375-825, 400-825, 425-825, 450-825, 475-825,500-825, 525-825, 550-825, 575-825, 600-825, 625-825, 650-825, 675-825,700-825, 725-825, 750-825, 775-825, 800-825, 1-800, 25-800, 50-800,75-800, 100-800, 125-800, 150-800, 175-800, 200-800, 225-800, 250-800,275-800, 300-800, 325-800, 350-800, 375-800, 400-800, 425-800, 450-800,475-800, 500-800, 525-800, 550-800, 575-800, 600-800, 625-800, 650-800,675-800, 700-800, 725-800, 750-800, 775-800, 1-775, 25-775, 50-775,75-775, 100-775, 125-775, 150-775, 175-775, 200-775, 225-775, 250-775,275-775, 300-775, 325-775, 350-775, 375-775, 400-775, 425-775, 450-775,475-775, 500-775, 525-775, 550-775, 575-775, 600-775, 625-775, 650-775,675-775, 700-775, 725-775, 750-775, 1-750, 25-750, 50-750, 75-750,100-750, 125-750, 150-750, 175-750, 200-750, 225-750, 250-750, 275-750,300-750, 325-750, 350-750, 375-750, 400-750, 425-750, 450-750, 475-750,500-750, 525-750, 550-750, 575-750, 600-750, 625-750, 650-750, 675-750,700-750, 725-750, 1-725, 25-725, 50-725, 75-725, 100-725, 125-725,150-725, 175-725, 200-725, 225-725, 250-725, 275-725, 300-725, 325-725,350-725, 375-725, 400-725, 425-725, 450-725, 475-725, 500-725, 525-725,550-725, 575-725, 600-725, 625-725, 650-725, 675-725, 700-725, 1-700,25-700, 50-700, 75-700, 100-700, 125-700, 150-700, 175-700, 200-700,225-700, 250-700, 275-700, 300-700, 325-700, 350-700, 375-700, 400-700,425-700, 450-700, 475-700, 500-700, 525-700, 550-700, 575-700, 600-700,625-700, 650-700, 675-700, 1-675, 25-675, 50-675, 75-675, 100-675,125-675, 150-675, 175-675, 200-675, 225-675, 250-675, 275-675, 300-675,325-675, 350-675, 375-675, 400-675, 425-675, 450-675, 475-675, 500-675,525-675, 550-675, 575-675, 600-675, 625-675, 650-675, 1-650, 25-650,50-650, 75-650, 100-650, 125-650, 150-650, 175-650, 200-650, 225-650,250-650, 275-650, 300-650, 325-650, 350-650, 375-650, 400-650, 425-650,450-650, 475-650, 500-650, 525-650, 550-650, 575-650, 600-650, 625-650,1-625, 25-625, 50-625, 75-625, 100-625, 125-625, 150-625, 175-625,200-625, 225-625, 250-625, 275-625, 300-625, 325-625, 350-625, 375-625,400-625, 425-625, 450-625, 475-625, 500-625, 525-625, 550-625, 575-625,600-625, 1-600, 25-600, 50-600, 75-600, 100-600, 125-600, 150-600,175-600, 200-600, 225-600, 250-600, 275-600, 300-600, 325-600, 350-600,375-600, 400-600, 425-600, 450-600, 475-600, 500-600, 525-600, 550-600,575-600, 1-575, 25-575, 50-575, 75-575, 100-575, 125-575, 150-575,175-575, 200-575, 225-575, 250-575, 275-575, 300-575, 325-575, 350-575,375-575, 400-575, 425-575, 450-575, 475-575, 500-575, 525-575, 550-575,1-550, 25-550, 50-550, 75-550, 100-550, 125-550, 150-550, 175-550,200-550, 225-550, 250-550, 275-550, 300-550, 325-550, 350-550, 375-550,400-550, 425-550, 450-550, 475-550, 500-550, 525-550, 1-525, 25-525,50-525, 75-525, 100-525, 125-525, 150-525, 175-525, 200-525, 225-525,250-525, 275-525, 300-525, 325-525, 350-525, 375-525, 400-525, 425-525,450-525, 475-525, 500-525, 1-500, 25-500, 50-500, 75-500, 100-500,125-500, 150-500, 175-500, 200-500, 225-500, 250-500, 275-500, 300-500,325-500, 350-500, 375-500, 400-500, 425-500, 450-500, 475-500, 1-475,25-475, 50-475, 75-475, 100-475, 125-475, 150-475, 175-475, 200-475,225-475, 250-475, 275-475, 300-475, 325-475, 350-475, 375-475, 400-475,425-475, 450-475, 1-450, 25-450, 50-450, 75-450, 100-450, 125-450,150-450, 175-450, 200-450, 225-450, 250-450, 275-450, 300-450, 325-450,350-450, 375-450, 400-450, 425-450, 1-425, 25-425, 50-425, 75-425,100-425, 125-425, 150-425, 175-425, 200-425, 225-425, 250-425, 275-425,300-425, 325-425, 350-425, 375-425, 400-425, 1-400, 25-400, 50-400,75-400, 100-400, 125-400, 150-400, 175-400, 200-400, 225-400, 250-400,275-400, 300-400, 325-400, 350-400, 375-400, 1-375, 25-375, 50-375,75-375, 100-375, 125-375, 150-375, 175-375, 200-375, 225-375, 250-375,275-375, 300-375, 325-375, 350-375, 1-350, 25-350, 50-350, 75-350,100-350, 125-350, 150-350, 175-350, 200-350, 225-350, 250-350, 275-350,300-350, 325-350, 1-325, 25-325, 50-325, 75-325, 100-325, 125-325,150-325, 175-325, 200-325, 225-325, 250-325, 275-325, 300-325, 1-300,25-300, 50-300, 75-300, 100-300, 125-300, 150-300, 175-300, 200-300,225-300, 250-300, 275-300, 1-275, 25-275, 50-275, 75-275, 100-275,125-275, 150-275, 175-275, 200-275, 225-275, 250-275, 1-250, 25-250,50-250, 75-250, 100-250, 125-250, 150-250, 175-250, 200-250, 225-250,1-225, 25-225, 50-225, 75-225, 100-225, 125-225, 150-225, 175-225,200-225, 1-200, 25-200, 50-200, 75-200, 100-200, 125-200, 150-200,175-200, 1-175, 25-175, 50-175, 75-175, 100-175, 125-175, 150-175,1-150, 25-150, 50-150, 75-150, 100-150, 125-150, 1-125, 25-125, 50-125,75-125, 100-125, 1-100, 25-100, 50-100, 75-100, 1-75, 25-75, 50-75,1-50, 25-50, and/or 1-25 of SEQ ID NO:18.

In certain additional preferred embodiments, polynucleotides of theinvention comprise, or alternatively, consist of nucleotide residues400-627, 425-627, 450-627, 475-627, 500-627, 525-627, 550-627, 575-627,600-627, 400-600, 425-600, 450-600, 475-600, 500-600, 525-600, 550-600,575-600, 400-575, 425-575, 450-575, 475-575, 500-575, 525-575, 550-575,400-550, 425-550, 450-550, 475-550, 500-550, 525-550, 400-500, 425-500,450-500, 475-500, 400-475, 425-475, 450-475, 400-450, 425-450, 571-800,600-800, 625-800, 650-800, 675-800, 700-800, 725-800, 750-800, 775-800,571-775, 600-775, 625-775, 650-775, 675-775, 700-775, 725-775, 750-775,571-750, 600-750, 625-750, 650-750, 675-750, 700-750, 725-750, 571-725,600-725, 625-725, 650-725, 675-725, 700-725, 571-700, 600-700, 625-700,650-700, 675-700, 571-675, 600-675, 625-675, 650-675, 571-650, 600-650,625-650, 571-625, 600-625, and/or 571-600 of SEQ ID NO:1.

In additional preferred embodiments, polynucleotides of the inventioncomprise, or alternatively, consist of nucleotide residues 147-500,147-450, 147-400, 147-350, 200-500, 200-450, 200-400, 200-350, 250-500,250-450, 250-400, 250-350, 300-500, 300-450, 300-400, 300-350, 350-750,350-700, 350-650, 350-600, 350-550, 400-750, 400-700, 400-650, 400-600,400-550, 425-750, 425-700, 425-650, 425-600, 425-550, 450-1020,450-1001, 450-950, 450-900, 450-850, 450-800, 450-775, 500-1001,500-950, 500-900, 500-850, 500-800, 500-775, 550-1001, 550-950, 550-900,550-850, 550-800, 550-775, 600-1001, 600-950, 600-900, 600-850, 600-800,600-775, 650-1001, 650-950, 650-900, 650-850, 650-800, 650-775,700-1001, 700-950, 700-900, 700-850, 700-800, 700-775, 825-1082,850-1082, 875-1082, 900-1082, 925-1082, 950-1082, 975-1082, 1000-1082,1025-1082, and/or 1050-1082 of SEQ ID NO:1.

Preferably, the polynucleotide fragments of the invention encode apolypeptide which demonstrates a Neutrokine-alpha and/orNeutrokine-alphaSV functional activity. By a polypeptide demonstrating“functional activity” is meant, a polypeptide capable of displaying oneor more known functional activities associated with a full-length and/orsecreted Neutrokine-alpha polypeptide and/or Neutrokine-alphaSVpolypeptide. Such functional activities include, but are not limited to,biological activity (e.g., ability to stimulate B cell proliferation,survival, differentiation, and/or activation), antigenicity [ability tobind (or compete with a Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide for binding) to an anti-Neutrokine-alpha and/oranti-Neutrokine-alphaSV antibody], immunogenicity (ability to generateantibody which binds to a Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide), ability to form multimers with Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention, and ability to bind toa receptor or ligand for a Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide.

In additional specific embodiments, the polynucleotide fragments of theinvention encode a polypeptide comprising, or alternatively, consistingof the predicted intracellular domain (amino acids 1 to 46 of SEQ IDNO:2), the predicted transmembrane domain (amino acids 47 to 72 of SEQID NO:2), the predicted extracellular domain (amino acids 73 to 285 ofSEQ ID NO:2), or the predicted TNF conserved domain (amino acids 191 to284 of SEQ ID NO:2) of Neutrokine-alpha. In additional embodiments, thepolynucleotide fragments of the invention encode a polypeptidecomprising, or alternatively, consisting of any combination of 1, 2, 3,or all 4 of the above recited domains. Polypeptides encoded by thesepolynucleotides are also encompassed by the invention.

In additional specific embodiments, the polynucleotide fragments of theinvention encode a polypeptide comprising, or alternatively, consistingof the predicted intracellular domain (amino acids 1 to 46 of SEQ IDNO:19), the predicted transmembrane domain (amino acids 47 to 72 of SEQID NO:19), the predicted extracellular domain (amino acids 73 to 266 ofSEQ ID NO:19), or the predicted TNF conserved domain (amino acids 172 to265 of SEQ ID NO:19) of Neutrokine-alphaSV. In additional embodiments,the polynucleotide fragments of the invention encode a polypeptidecomprising, or alternatively, consisting of any combination of 1, 2, 3,or all 4 of the above recited domains. Polypeptides encoded by thesepolynucleotides are also encompassed by the invention.

In another embodiment, polynucleotide fragments of the inventioncomprise, or alternatively consist of, polynucleotides which encode anamino acid sequence selected from residues Met-1 to Lys-113, Leu-114 toThr-141, Ile-142 to Lys-160, Gly-161 to Gln-198, Val-199 to Ala-248, andGly-250 to Leu-285 of SEQ ID NO:2. Moreover, polynucleotides that encodeany combination of two, three, four, five or more of these amino acidsequences are also encompassed by the invention. Polypeptides encoded bythese polynucleotides are also encompassed by the invention.

In another embodiment, polynucleotide fragments of the inventioncomprise, or alternatively consist of, polynucleotides which encode anamino acid sequence selected from residues Met-1 to Lys 113, Leu-114 toThr-141, Gly-142 to Gln-179, Val-180 to Ala-229, and Gly-230 to Leu-266of SEQ ID NO:19. Moreover, polynucleotides that encode any combinationof two, three, four, five or more of these amino acid sequences are alsoencompassed by the invention. Polypeptides encoded by thesepolynucleotides are also encompassed by the invention.

In another embodiment, polynucleotide fragments of the inventioncomprise, or alternatively consist of, polynucleotides which encode anamino acid sequence selected from residues Met-1 to Lys-106, Leu-107 toThr-134, Glu-135 to Asn-165, Ile-167 to Lys-184, Gly-185 to Gln-224,Val-225 to Ala-272, and Gly-273 to Leu-309 of SEQ ID NO:23. Moreover,polynucleotides that encode any combination of two, three, four, five ormore of these amino acid sequences are also encompassed by theinvention. Polypeptides encoded by these polynucleotides are alsoencompassed by the invention.

In another embodiment, polynucleotide fragments of the inventioncomprise, or alternatively consist of, polynucleotides which encode anamino acid sequence selected from residues Tyr-1 to Lys-47, Leu-48 toThr-75, Ile-76 to Lys-94, Gly-95 to Gln-132, Val-133 to Ala-182, andGly-183 to Ala-219 of SEQ ID NO:28. Moreover, polynucleotides thatencode any combination of two, three, four, five or more of these aminoacid sequences are also encompassed by the invention. Polypeptidesencoded by these polynucleotides are also encompassed by the invention.

In another embodiment, polynucleotide fragments of the inventioncomprise, or alternatively consist of, polynucleotides which encode anamino acid sequence selected from residues Tyr-1 to Lys-47, Leu-48 toThr-75, Ile-76 to Lys-94, Gly-95 to Gln-132, Val-133 to Ala-182, andGly-183 to Ala-219 of SEQ ID NO:30. Moreover, polynucleotides thatencode any combination of two, three, four, five or more of these aminoacid sequences are also encompassed by the invention. Polypeptidesencoded by these polynucleotides are also encompassed by the invention.

In another embodiment, the polynucleotides of the invention comprise, oralternatively consist of, the sequence shown in SEQ ID NO:21. Thesequence shown as SEQ ID NO:21 encodes a polypeptide consisting of aninitiating methionine residue linked to residues Ala-134 through Leu-285of the Neutrokine-alpha polypeptide sequence shown as SEQ ID NO:2.Polypeptides encoded by these polynucleotides are also encompassed bythe invention.

In certain additional preferred embodiments, polynucleotides of theinvention comprise, or alternatively, consist of nucleotide residues1-459, 15-459, 30-459, 45-459, 60-459, 75-459, 90-459, 105-459, 120-459,135-459, 150-459, 165-459, 180-459, 195-459, 210-459, 225-459, 240-459,255-459, 270-459, 285-459, 300-459, 315-459, 330-459, 345-459, 360-459,375-459, 390-459, 405-459, 420-459, 435-459, 450-459, 1-450, 15-450,30-450, 45-450, 60-450, 75-450, 90-450, 105-450, 120-450, 135-450,150-450, 165-450, 180-450, 195-450, 210-450, 225-450, 240-450, 255-450,270-450, 285-450, 300-450, 315-450, 330-450, 345-450, 360-450, 375-450,390-450, 405-450, 420-450, 435-450, 1-435, 15-435, 30-435, 45-435,60-435, 75-435, 90-435, 105-435, 120-435, 135-435, 150-435, 165-435,180-435, 195-435, 210-435, 225-435, 240-435, 255-435, 270-435, 285-435,300-435, 315-435, 330-435, 345-435, 360-435, 375-435, 390-435, 405-435,420-435, 1-420, 15-420, 30-420, 45-420, 60-420, 75-420, 90-420, 105-420,120-420, 135-420, 150-420, 165-420, 180-420, 195-420, 210-420, 225-420,240-420, 255-420, 270-420, 285-420, 300-420, 315-420, 330-420, 345-420,360-420, 375-420, 390-420, 405-420, 1-405, 15-405, 30-405, 45-405,60-405, 75-405, 90-405, 105-405, 120-405, 135-405, 150-405, 165-405,180-405, 195-405, 210-405, 225-405, 240-405, 255-405, 270-405, 285-405,300-405, 315-405, 330-405, 345-405, 360-405, 375-405, 390-405, 1-390,15-390, 30-390, 45-390, 60-390, 75-390, 90-390, 105-390, 120-390,135-390, 150-390, 165-390, 180-390, 195-390, 210-390, 225-390, 240-390,255-390, 270-390, 285-390, 300-390, 315-390, 330-390, 345-390, 360-390,375-390, 1-375, 15-375, 30-375, 45-375, 60-375, 75-375, 90-375, 105-375,120-375, 135-375, 150-375, 165-375, 180-375, 195-375, 210-375, 225-375,240-375, 255-375, 270-375, 285-375, 300-375, 315-375, 330-375, 345-375,360-375, 1-360, 15-360, 30-360, 45-360, 60-360, 75-360, 90-360, 105-360,120-360, 135-360, 150-360, 165-360, 180-360, 195-360, 210-360, 225-360,240-360, 255-360, 270-360, 285-360, 300-360, 315-360, 330-360, 345-360,1-345, 15-345, 30-345, 45-345, 60-345, 75-345, 90-345, 105-345, 120-345,135-345, 150-345, 165-345, 180-345, 195-345, 210-345, 225-345, 240-345,255-345, 270-345, 285-345, 300-345, 315-345, 330-345, 1-330, 15-330,30-330, 45-330, 60-330, 75-330, 90-330, 105-330, 120-330, 135-330,150-330, 165-330, 180-330, 195-330, 210-330, 225-330, 240-330, 255-330,270-330, 285-330, 300-330, 315-330, 1-315, 15-315, 30-315, 45-315,60-315, 75-315, 90-315, 105-315, 120-315, 135-315, 150-315, 165-315,180-315, 195-315, 210-315, 225-315, 240-315, 255-315, 270-315, 285-315,300-315, 1-300, 15-300, 30-300, 45-300, 60-300, 75-300, 90-300, 105-300,120-300, 135-300, 150-300, 165-300, 180-300, 195-300, 210-300, 225-300,240-300, 255-300, 270-300, 285-300, 1-285, 15-285, 30-285, 45-285,60-285, 75-285, 90-285, 105-285, 120-285, 135-285, 150-285, 165-285,180-285, 195-285, 210-285, 225-285, 240-285, 255-285, 270-285, 1-270,15-270, 30-270, 45-270, 60-270, 75-270, 90-270, 105-270, 120-270,135-270, 150-270, 165-270, 180-270, 195-270, 210-270, 225-270, 240-270,255-270, 1-255, 15-255, 30-255, 45-255, 60-255, 75-255, 90-255, 105-255,120-255, 135-255, 150-255, 165-255, 180-255, 195-255, 210-255, 225-255,240-255, 1-240, 15-240, 30-240, 45-240, 60-240, 75-240, 90-240, 105-240,120-240, 135-240, 150-240, 165-240, 180-240, 195-240, 210-240, 225-240,1-225, 15-225, 30-225, 45-225, 60-225, 75-225, 90-225, 105-225, 120-225,135-225, 150-225, 165-225, 180-225, 195-225, 210-225, 1-210, 15-210,30-210, 45-210, 60-210, 75-210, 90-210, 105-210, 120-210, 135-210,150-210, 165-210, 180-210, 195-210, 1-195, 15-195, 30-195, 45-195,60-195, 75-195, 90-195, 105-195, 120-195, 135-195, 150-195, 165-195,180-195, 1-180, 15-180, 30-180, 45-180, 60-180, 75-180, 90-180, 105-180,120-180, 135-180, 150-180, 165-180, 1-165, 15-165, 30-165, 45-165,60-165, 75-165, 90-165, 105-165, 120-165, 135-165, 150-165, 1-150,15-150, 30-150, 45-150, 60-150, 75-150, 90-150, 105-150, 120-150,135-150, 1-135, 15-135, 30-135, 45-135, 60-135, 75-135, 90-135, 105-135,120-135, 1-120, 15-120, 30-120, 45-120, 60-120, 75-120, 90-120, 105-120,1-105, 15-105, 30-105, 45-105, 60-105, 75-105, 90-105, 1-90, 15-90,30-90, 45-90, 60-90, 75-90, 1-75, 15-75, 30-75, 45-75, 60-75, 1-60,15-60, 30-60, 45-60, 1-45, 15-45, 30-45, 1-30, and/or 15-30 of SEQ IDNO:21. Polypeptides encoded by these polynucleotides are alsoencompassed by the invention.

Accordingly, specific embodiments of the invention are directed topolynucleotides encoding polypeptides which comprise, or alternativelyconsist of, the amino acid sequence of beta pleated sheet region A, A′,B, B′, C, D, E, F, G, or H disclosed in FIGS. 7A-1 and 7A-2 anddescribed in Example 6. Additional embodiments of the invention aredirected to polynucleotides encoding Neutrokine-alpha polypeptides whichcomprise, or alternatively consist of, any combination of 1, 2, 3, 4, 5,6, 7, 8, 9 or all 10 of beta pleated sheet regions A-H disclosed inFIGS. 7A-1 and 7A-2 and described in Example 6. Additional preferredembodiments of the invention are directed to polypeptides whichcomprise, or alternatively consist of, the Neutrokine-alpha amino acidsequence of beta pleated sheet region A, A′, B, B′, C, D, E, F, G, or Hdisclosed in FIGS. 7A-1 and 7A-2 and described in Example 6. Additionalembodiments of the invention are directed Neutrokine-alpha polypeptideswhich comprise, or alternatively consist of, any combination of 1, 2, 3,4, 5, 6, 7, 8, 9 or all 10 of beta pleated sheet regions A through Hdisclosed in FIGS. 7A-1 and 7A-2 and described in Example 6.

In certain other preferred embodiments, polynucleotides of the inventioncomprise, or alternatively consist of, nucleotide residues 34-57,118-123, 133-141, 151-159, 175-216, 232-255, 280-315, 328-357, 370-393,and/or 430-456 of SEQ ID NO:21. Polypeptides encoded by thesepolynucleotides are also encompassed by the invention. Thesepolynucleotide and polypeptide fragments correspond to the predictedbeta-pleated sheet regions shown in FIGS. 7A-1 and 7A-2. In certainembodiments, polynucleotides of the invention comprise, or alternativelyconsist of, a polynucleotide sequence at least 90%, 95%, 96%, 97%, 98%or 99% identical to the polynucleotide sequence encoding one, two,three, four, five, six, seven, eight, nine or ten of the beta-pleatedsheet regions described above. The present invention also encompassesthe above polynucleotide sequences fused to a heterologouspolynucleotide sequence. Polypeptides encoded by these polynucleotidesequences are also encompassed by the invention. In another embodiment,the invention provides an isolated nucleic acid molecule comprising apolynucleotide which hybridizes under stringent hybridization conditionsto one, two, three, four, five, six, seven, eight, nine or ten of thebeta-pleated sheet polynucleotides of the invention described above. Themeaning of the phrase “stringent conditions” as used herein is describedinfra.

In further preferred embodiments, polynucleotides of the inventioncomprise, or alternatively consist of, nucleotide residues 576-599,660-665, 675-683, 693-701, 717-758, 774-803, 822-857, 870-899, 912-935,and/or 972-998 of SEQ ID NO:1. Polypeptides encoded by thesepolynucleotide fragments are also encompassed by the invention. Thesepolynucleotide and polypeptide fragments correspond to the predictedbeta-pleated sheet regions shown in FIGS. 7A-1 and 7A-2.

In additional preferred embodiments, polynucleotides of the inventioncomprise, or alternatively consist of, nucleotide residues 457-462,472-480, 490-498, 514-555, 571-600, 619-654, 667-696, 699-732, and/or769-795 of SEQ ID NO:18. Polypeptides encoded by these polynucleotidefragments are also encompassed by the invention. These polynucleotideand polypeptide fragments correspond to the predicted beta-pleated sheetregions shown in FIGS. 7A-1 and 7A-2.

In yet further preferred embodiments, polynucleotides of the inventioncomprise, or alternatively consist of, nucleotide residues 124-129,139-147, 157-165, 181-222, 238-267, 286-321, 334-363, 376-399, and/or436-462 of SEQ ID NO:22. Polypeptides encoded by these polynucleotidefragments are also encompassed by the invention. These polynucleotideand polypeptide fragments correspond to the predicted beta-pleated sheetregions shown in FIGS. 7A-1 and 7A-2. Polypeptides comprising, oralternatively, consisting of the amino acid sequence of any combinationof one, two, three, four, five, six, seven, eight, nine, ten, or all ofthese regions are encompassed by the invention.

The relative positions of several intron/exon boundaries were determinedfor the mouse Neutrokine-alpha (SEQ ID NO:22 and SEQ ID NO:23) based onsequence analysis of mouse genomic DNA. The apparent second exon fromthe 5′ end of the mouse Neutrokine-alpha genomic clone (preliminarilydesignated “Exon 2”) consists of Tyr-187 to Gln-222 of the sequenceshown in SEQ ID NO:23. The apparent third exon from the 5′ end of themouse Neutrokine-alpha genomic clone (preliminarily designated “Exon 3”)comprises Val-223 to Gly-273 of the sequence shown in SEQ ID NO:23.

Thus, in one embodiment, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, the amino acidsequence of residues Tyr-187 to Gln-222 of SEQ ID NO:23. The presentinvention is also directed to nucleic acid molecules comprising, oralternatively, consisting of, a polynucleotide sequence at least 80%,85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the polynucleotidesequence encoding the mouse Neutrokine-alpha polypeptides describedabove. The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these nucleic acids and/or polynucleotide sequences are alsoencompassed by the invention.

In another embodiment, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, the amino acidsequence of residues Val-223 to Gly-273 of SEQ ID NO:23. The presentinvention is also directed to nucleic acid molecules comprising, oralternatively, consisting of, a polynucleotide sequence at least 80%,85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the polynucleotidesequence encoding the mouse Neutrokine-alpha polypeptides describedabove. The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these nucleic acids and/or polynucleotide sequences are alsoencompassed by the invention.

Moreover, the relative positions of the corresponding intron/exonboundaries were determined for human Neutrokine-alpha (SEQ ID NO:1 andSEQ ID NO:2) based on an alignment of the sequences of mouse and humanNeutrokine-alpha polypeptides. The apparent second exon from the 5′ endof human Neutrokine-alpha (also preliminarily designated “Exon 2”)consists of, Tyr-163 to Gln-198 of the sequence shown in SEQ ID NO:2.The apparent third exon from the 5′ end of human Neutrokine-alpha (alsopreliminarily designated “Exon 3”) consists of, Val-199 to Gly-249 ofthe sequence shown in SEQ ID NO:2.

Thus, in one embodiment, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, the amino acidsequence of residues Tyr-163 to Gln-198 of SEQ ID NO:2. The presentinvention is also directed to nucleic acid molecules comprising, oralternatively, consisting of, a polynucleotide sequence at least 80%,85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the polynucleotidesequence encoding the Neutrokine-alpha polypeptides described above. Thepresent invention also encompasses the above polynucleotide sequencesfused to a heterologous polynucleotide sequence. Polypeptides encoded bythese nucleic acids and/or polynucleotide sequences are also encompassedby the invention.

In another embodiment, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, the amino acidsequence of residues Val-199 to Gly-249 of SEQ ID NO:2. The presentinvention is also directed to nucleic acid molecules comprising, oralternatively, consisting of, a polynucleotide sequence at least 80%,85%, 90%, 95%, 96%, 97%, 98% or 99% identical to the polynucleotidesequence encoding the Neutrokine-alpha polypeptides described above. Thepresent invention also encompasses the above polynucleotide sequencesfused to a heterologous polynucleotide sequence. Polypeptides encoded bythese nucleic acids and/or polynucleotide sequences are also encompassedby the invention.

The functional activity of Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides, and fragments, variants derivatives, and analogs thereof,can be assayed by various methods as described herein and as are wellknown in the art.

For example, in one embodiment where one is assaying for the ability tobind or compete with full-length Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide for binding to anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibody or binding to Neutrokine-alphareceptor(s) and/or Neutrokine-alphaSV receptor(s) on B cells, variousimmunoassays known in the art can be used, including but not limited to,competitive and non-competitive assay systems using techniques such asradioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich”immunoassays, immunoradiometric assays, gel diffusion precipitationreactions, immunodiffusion assays, in situ immunoassays (using colloidalgold, enzyme or radioisotope labels, for example), western blots,precipitation reactions, agglutination assays (e.g., gel agglutinationassays, hemagglutination assays), complement fixation assays,immunofluorescence assays, protein A assays, and immunoelectrophoresisassays, etc. In one embodiment, antibody binding is detected bydetecting a label on the primary antibody. In another embodiment, theprimary antibody is detected by detecting binding of a secondaryantibody or reagent to the primary antibody. In a further embodiment,the secondary antibody is labeled. Many means are known in the art fordetecting binding in an immunoassay and are within the scope of thepresent invention.

In another embodiment, where a Neutrokine-alpha and/orNeutrokine-alphaSV ligand is identified, or the ability of a polypeptidefragment, variant or derivative of the invention to multimerize is beingevaluated, binding can be assayed, e.g., by means well-known in the art,such as, for example, reducing and non-reducing gel chromatography,protein affinity chromatography, and affinity blotting. See generally,Phizicky, E., et al., 1995, Microbiol. Rev. 59:94-123. In anotherembodiment, physiological correlates of Neutrokine-alpha and/orNeutrokine-alphaSV binding to its substrates (signal transduction) canbe assayed.

In addition, assays described herein (see, e.g., Examples 6 and 7) andotherwise known in the art may routinely be applied to measure theability of Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides andfragments, variants derivatives and analogs thereof to elicitNeutrokine-alpha and/or Neutrokine-alphaSV related biological activity(e.g., to stimulate, or alternatively to inhibit (in the case ofNeutrokine-alpha and/or Neutrokine-alphaSV antagonists) B cellproliferation, differentiation and/or activation and/or to extend B cellsurvival in vitro or in vivo).

Other methods will be known to the skilled artisan and are within thescope of the invention.

In additional embodiments, the polynucleotides of the invention encodepolypeptides comprising, or alternatively consisting of, functionalattributes of Neutrokine-alpha and Neutrokine-alphaSV. Preferredembodiments of the invention in this regard include fragments thatcomprise, or alternatively consist of, alpha-helix and alpha-helixforming regions (“alpha-regions”), beta-sheet and beta-sheet formingregions (“beta-regions”), turn and turn-forming regions(“turn-regions”), coil and coil-forming regions (“coil-regions”),hydrophilic regions, hydrophobic regions, alpha amphipathic regions,beta amphipathic regions, flexible regions, surface-forming regions andhigh antigenic index regions of Neutrokine-alpha and Neutrokine-alphaSVpolypeptides.

It is believed one or more of the beta pleated sheet regions ofNeutrokine-alpha disclosed in FIGS. 7A-1 and 7A-2 is important fordimerization and also for interactions between Neutrokine-alpha and itsligands.

Certain preferred regions in this regard are set out in FIG. 3 (Table1). The data presented in FIG. 3 and that presented in Table I, merelypresent a different format of the same results obtained when the aminoacid sequence of SEQ ID NO:2 is analyzed using the default parameters ofthe DNA*STAR computer algorithm.

The above-mentioned preferred regions set out in FIG. 3 and in Table Iinclude, but are not limited to, regions of the aforementioned typesidentified by analysis of the amino acid sequence set out in FIGS. 1Aand 1B. As set out in FIG. 3 and in Table I, such preferred regionsinclude Garnier-Robson alpha-regions, beta-regions, turn-regions, andcoil-regions, Chou-Fasman alpha-regions, beta-regions, and coil-regions,Kyte-Doolittle hydrophilic regions and hydrophobic regions, Eisenbergalpha- and beta-amphipathic regions, Karplus-Schulz flexible regions,Emini surface-forming regions and Jameson-Wolf regions of high antigenicindex. Among highly preferred polynucleotides in this regard are thosethat encode polypeptides comprising, or alternatively consisting of,regions of Neutrokine-alpha and/or Neutrokine-alphaSV that combineseveral structural features, such as several (e.g., 1, 2, 3 or 4) of thefeatures set out above. Polypeptides encoded by the polynucleotides arealso encompassed by the invention.

Additionally, the data presented in columns VIII, IX, XIII, and XIV ofTable I can routinely be used to determine regions of Neutrokine-alphawhich exhibit a high degree of potential for antigenicity (column VIIIof Table I represents hydrophilicity according to Kyte-Doolittle; columnIX of Table I represents hydrophobicity according to Hopp-Woods; columnXIII of Table I represents antigenic index according to Jameson-Wolf;and column XIV of Table I represents surface probability according toEmini). Regions of high antigenicity are determined from the datapresented in columns VIII, IX, XIII, and/or IV by choosing values whichrepresent regions of the polypeptide which are likely to be exposed onthe surface of the polypeptide in an environment in which antigenrecognition may occur in the process of initiation of an immuneresponse. The data presented in FIG. 6 can also routinely be presentedin a similar tabular format by simply examining the amino acid sequencedisclosed in FIG. 6 (SEQ ID NO:19) using the modules and algorithms ofthe DNA*STAR set on default parameters. As above, the amino acidsequence presented in FIG. 6 can also be used to determine regions ofNeutrokine-alpha which exhibit a high degree of potential forantigenicity whether presented as a Figure (as in FIG. 6) or a table (asin Table 1).

TABLE I Res Position I II III IV V VI VII VIII IX X XI XII XIII XIV Met1 A . . . . . . 0.73 −0.71 . . . 0.95 1.39 Asp 2 A . . . . T . 1.12−0.66 * . . 1.15 1.56 Asp 3 A . . . . T . 1.62 −1.09 * . . 1.15 2.12 Ser4 A . . . . T . 2.01 −1.51 . . . 1.15 4.19 Thr 5 A . . . . T . 2.40−2.13 . . F 1.30 4.35 Glu 6 A A . . . . . 2.70 −1.73 * * F 0.90 4.51 Arg7 A A . . . . . 2.81 −1.34 * * F 0.90 4.51 Glu 8 A A . . . . . 2.00−1.73 * * F 0.90 6.12 Gln 9 A A . . . . . 1.99 −1.53 * * F 0.90 2.91 Ser10 A . . B . . . 2.00 −1.04 * * F 0.90 2.15 Arg 11 A . . B . . . 1.33−0.66 * * F 0.90 1.66 Leu 12 A . . B . . . 0.41 −0.09 * * F 0.45 0.51Thr 13 A . . B . . . 0.46 0.20 * * F −0.15 0.32 Ser 14 A A . . . . .0.50 −0.19 * * . 0.30 0.32 Cys 15 A A . . . . . 0.91 −0.19 * * . 0.300.78 Leu 16 A A . . . . . 0.80 −0.87 * * F 0.90 1.06 Lys 17 A A . . . .. 1.61 −1.36 . * F 0.90 1.37 Lys 18 A A . . . . . 1.32 −1.74 . * F 0.904.44 Arg 19 A A . . . . . 1.67 −1.70 . * F 0.90 5.33 Glu 20 A A . . . .. 1.52 −2.39 . * F 0.90 5.33 Glu 21 A A . . . . . 2.38 −1.70 . * F 0.902.20 Met 22 A A . . . . . 2.33 −1.70 . * F 0.90 2.24 Lys 23 A A . . . .. 1.62 −1.70 * * F 0.90 2.24 Leu 24 A A . . . . . 0.66 −1.13 * * F 0.750.69 Lys 25 A A . . . . . 0.36 −0.49 . * F 0.45 0.52 Glu 26 A A . B . .. −0.53 −0.71 * * . 0.60 0.35 Cys 27 A A . B . . . −0.74 −0.03 * * .0.30 0.30 Val 28 A A . B . . . −1.00 −0.03 * * . 0.30 0.12 Ser 29 A A .B . . . −0.08 0.40 * * . −0.30 0.11 Ile 30 A . . B . . . −0.08 0.40 * *. −0.30 0.40 Leu 31 A . . B . . . −0.08 −0.17 * . . 0.45 1.08 Pro 32 . .. B . . C 0.29 −0.81 * . F 1.10 1.39 Arg 33 . . . . T . . 0.93 −0.81 . *F 1.50 2.66 Lys 34 . . . . T . . 0.93 −1.07 . . F 1.84 4.98 Glu 35 . . .. . . C 0.97 −1.37 * * F 1.98 4.32 Ser 36 . . . . . T C 1.89 −1.16 * * F2.52 1.64 Pro 37 . . . . . T C 1.80 −1.16 * * F 2.86 1.60 Ser 38 . . . .T T . 1.39 −0.77 * . F 3.40 1.24 Val 39 A . . . . T . 1.39 −0.39 . * F2.36 1.24 Arg 40 A . . . . . . 1.39 −0.77 * * F 2.46 1.60 Ser 41 A . . .. . . 1.34 −1.20 * * F 2.46 2.00 Ser 42 . . . . T T . 1.60 −1.16 . * F3.06 2.67 Lys 43 . . . . T T . 1.09 −1.80 . * F 3.06 2.72 Asp 44 . . . .T T . 1.13 −1.11 * * F 3.40 1.67 Gly 45 A . . . . T . 0.43 −0.81 * * F2.66 1.03 Lys 46 A A . . . . . 0.14 −0.70 . . F 1.77 0.52 Leu 47 A A . .. . . 0.13 −0.20 * . . 0.98 0.31 Leu 48 A A . . . . . −0.72 0.29 * . .0.04 0.46 Ala 49 A A . . . . . −1.53 0.54 . * . −0.60 0.19 Ala 50 A A .. . . . −2.00 1.23 . . . −0.60 0.19 Thr 51 A A . . . . . −2.63 1.23 . .. −0.60 0.19 Leu 52 A A . . . . . −2.63 1.04 . . . −0.60 0.19 Leu 53 A A. . . . . −2.63 1.23 . . . −0.60 0.15 Leu 54 A A . . . . . −2.34 1.41 .. . −0.60 0.09 Ala 55 A A . . . . . −2.42 1.31 . . . −0.60 0.14 Leu 56 AA . . . . . −2.78 1.20 . . . −0.60 0.09 Leu 57 A . . . . T . −2.78 1.09. . . −0.20 0.06 Ser 58 A . . . . T . −2.28 1.09 . . . −0.20 0.05 Cys 59A . . . . T . −2.32 1.07 . . . −0.20 0.09 Cys 60 A . . . . T . −2.591.03 . . . −0.20 0.08 Leu 61 . . B B . . . −2.08 0.99 . . . −0.60 0.04Thr 62 . . B B . . . −1.97 0.99 . . . −0.60 0.11 Val 63 . . B B . . .−1.91 1.20 . . . −0.60 0.17 Val 64 . . B B . . . −1.24 1.39 . . . −0.600.33 Ser 65 . . B B . . . −1.43 1.10 . . . −0.60 0.40 Phe 66 A . . B . .. −1.21 1.26 . . . −0.60 0.40 Tyr 67 A . . B . . . −1.49 1.11 . . .−0.60 0.54 Gln 68 A . . B . . . −1.44 0.97 . . . −0.60 0.41 Val 69 A . .B . . . −0.59 1.27 . . . −0.60 0.39 Ala 70 A . . B . . . −0.63 0.89 . .. −0.60 0.43 Ala 71 A . . B . . . 0.07 0.56 . * . −0.60 0.25 Leu 72 A .. . . T . −0.50 0.16 . * . 0.10 0.55 Gln 73 A . . . . T . −1.09 0.20 . .F 0.25 0.45 Gly 74 A . . . . T . −0.53 0.20 . . F 0.25 0.45 Asp 75 A . .. . T . −0.76 0.09 . * F 0.25 0.73 Leu 76 A A . . . . . −0.06 0.09 . * F−0.15 0.35 Ala 77 A A . . . . . 0.17 −0.31 . * . 0.30 0.69 Ser 78 A A .. . . . 0.17 −0.24 . * . 0.30 0.42 Leu 79 A A . . . . . −0.30 −0.24 . *. 0.30 0.88 Arg 80 A A . . . . . −0.30 −0.24 . * . 0.30 0.72 Ala 81 A A. . . . . 0.17 −0.34 . * . 0.30 0.93 Glu 82 A A . . . . . 0.72 −0.30 . *. 0.45 1.11 Leu 83 A A . . . . . 0.99 −0.49 . * . 0.30 0.77 Gln 84 A A .. . . . 1.21 0.01 . * . −0.15 1.04 Gly 85 A A . . . . . 1.10 0.01 * * .−0.30 0.61 His 86 A A . . . . . 1.73 0.01 * * . −0.15 1.27 His 87 A A .. . . . 0.92 −0.67 . * . 0.75 1.47 Ala 88 A A . . . . . 1.52 −0.39 . * .0.45 1.22 Glu 89 A A . . . . . 0.93 −0.39 . . . 0.45 1.39 Lys 90 A A . .. . . 0.93 −0.39 * . F 0.60 1.03 Leu 91 A . . . . T . 0.38 −0.46 * . .0.85 1.01 Pro 92 A . . . . T . 0.07 −0.46 . . . 0.70 0.59 Ala 93 A . . .. T . 0.07 −0.03 . . . 0.70 0.29 Gly 94 A . . . . T . −0.14 0.47 . . .−0.20 0.36 Ala 95 A . . . . . . −0.14 0.21 . * . −0.10 0.36 Gly 96 A . .. . . . 0.08 −0.21 . . F 0.65 0.71 Ala 97 A . . . . . . −0.06 −0.21 . .F 0.65 0.72 Pro 98 A . . . . . . −0.28 −0.21 . * F 0.65 0.71 Lys 99 A A. . . . . 0.07 −0.03 . . F 0.45 0.59 Ala 100 A A . . . . . 0.66 −0.46 .. F 0.60 1.01 Gly 101 A A . . . . . 0.41 −0.96 . . F 0.90 1.13 Leu 102 AA . . . . . 0.79 −0.89 . . F 0.75 0.57 Glu 103 A A . . . . . 0.41−0.46 * . F 0.45 0.88 Glu 104 A A . . . . . −0.49 −0.46 * . F 0.45 0.89Ala 105 A A . . . . . −0.21 −0.24 . . . 0.30 0.81 Pro 106 A A . . . . .−0.46 −0.44 . . . 0.30 0.67 Ala 107 A A . . . . . 0.01 0.06 . . . −0.300.39 Val 108 A A . . . . . −0.80 0.49 . * . −0.60 0.38 Thr 109 A A . . .. . −0.76 0.67 . * . −0.60 0.20 Ala 110 A A . . . . . −1.06 0.24 * * .−0.30 0.40 Gly 111 A A . . . . . −1.54 0.43 * * . −0.60 0.38 Leu 112 A A. . . . . −0.96 0.57 * * . −0.60 0.23 Lys 113 . A B . . . . −0.310.09 * * . −0.30 0.39 Ile 114 . A B . . . . −0.21 0.01 * . . −0.30 0.61Phe 115 . A B . . . . −0.21 0.01 * . . 0.15 1.15 Glu 116 . A . . . . C−0.08 −0.17 * . F 1.25 0.58 Pro 117 . A . . . . C 0.39 0.26 * * F 1.101.28 Pro 118 . . . . . . C 0.34 −0.00 . . F 2.20 1.47 Ala 119 . . . . .T C 0.89 −0.79 . * F 3.00 1.47 Pro 120 . . . . . T C 1.59 −0.36 . * F2.25 0.94 Gly 121 . . . . T T . 1.29 −0.39 . * F 2.15 0.98 Glu 122 . . .. T T . 1.20 −0.43 . . F 2.00 1.30 Gly 123 . . . . . . C 1.41 −0.54 . .F 1.60 1.12 Asn 124 . . . . . T C 2.00 −0.57 . . F 1.50 1.97 Ser 125 . .. . . T C 1.91 −0.60 . * F 1.50 1.82 Ser 126 . . . . . T C 2.37 −0.21. * F 1.54 2.47 Gln 127 . . . . . T C 2.37 −0.64 . * F 2.18 3.01 Asn 128. . . . . . C 2.76 −0.64 . . F 2.32 3.61 Ser 129 . . . . . T C 2.87−1.03 . . F 2.86 5.39 Arg 130 . . . . T T . 2.58 −1.41 * . F 3.40 6.09Asn 131 . . . . T T . 2.02 −1.31 * . F 3.06 3.83 Lys 132 . . . . T T .2.02 −1.07 * . F 2.72 2.12 Arg 133 . . . . T . . 1.68 −1.06 * . F 2.181.88 Ala 134 . . . . . . C 1.77 −0.63 * . F 1.64 1.15 Val 135 . . . . .. C 1.66 −0.60 * . F 1.49 0.89 Gln 136 . . . . . . C 1.66 −0.60 * . F1.83 0.79 Gly 137 . . . . . T C 1.30 −0.60 * . F 2.52 1.35 Pro 138 . . .. . T C 0.33 −0.61 * . F 2.86 2.63 Glu 139 . . . . T T . 0.61 −0.61 * .F 3.40 1.13 Glu 140 A . . . . T . 1.47 −0.53 * . F 2.66 1.64 Thr 141 A .. . . . . 1.47 −0.56 . . F 2.12 1.84 Val 142 A . . . . . . 1.14 −0.99 .. F 1.78 1.77 Thr 143 A . . . . T . 0.54 −0.41 . . F 1.19 0.55 Gln 144 A. . . . T . 0.54 0.27 * . F 0.25 0.31 Asp 145 A . . . . T . −0.27 0.19 *. F 0.25 0.73 Cys 146 A . . . . T . −0.84 0.23 * . . 0.10 0.42 Leu 147 AA . . . . . −0.58 0.43 * . . −0.60 0.17 Gln 148 A A . . . . . −0.270.53 * . . −0.60 0.10 Leu 149 A A . . . . . −0.57 0.53 * * . −0.30 0.32Ile 150 A A . . . . . −0.57 0.34 * . . 0.30 0.52 Ala 151 . A . . . . C−0.21 −0.34 . * . 1.40 0.52 Asp 152 . . . . T T . 0.39 −0.26 . * F 2.450.91 Ser 153 . . . . . T C 0.08 −0.51 . . F 3.00 2.00 Glu 154 . . . . .T C −0.00 −0.71 . . F 2.70 2.86 Thr 155 . . . . . T C 0.89 −0.53 * . F2.40 1.20 Pro 156 . . . B . . C 1.52 −0.13 * . F 1.56 1.55 Thr 157 . . .B T . . 1.18 −0.51 * . F 1.92 1.79 Ile 158 A . . B . . . 1.18 −0.09 . .F 1.08 1.23 Gln 159 . . . . T T . 0.93 −0.19 . . F 2.04 1.07 Lys 160 . .. . T T . 0.93 0.14 * . F 1.60 1.16 Gly 161 . . . . T T . 0.44 0.14 * .F 1.44 2.38 Ser 162 . . . . T T . −0.10 0.24 * . F 1.28 1.19 Tyr 163 . .. B T . . 0.58 0.49 * . . 0.12 0.44 Thr 164 . . B B . . . 0.29 0.91 * .. −0.44 0.69 Phe 165 . . B B . . . −0.57 1.40 * . . −0.60 0.54 Val 166 .. B B . . . −1.03 1.70 . . . −0.60 0.29 Pro 167 . . B B . . . −1.03 1.63. . . −0.60 0.16 Trp 168 A . . B . . . −1.49 1.53 . * . −0.60 0.25 Leu169 A . . B . . . −1.13 1.53 * . . −0.60 0.29 Leu 170 A . . B . . .−0.32 0.89 * . . -0.30 0.38 Ter 171 A . . . . . . 0.19 0.46 * . . 0.200.71 Phe 172 . . . . T . . 0.10 −0.03 * . . 1.80 0.85 Lys 173 . . . . TT . −0.20 −0.33 * . F 2.60 1.38 Arg 174 . . . . . T C −0.20 −0.51 . . F3.00 1.04 Gly 175 . . . . . T C 0.61 −0.21 . . F 2.25 0.99 Ser 176 A . .. . T . 0.91 −1.00 * . F 2.05 0.86 Ala 177 A A . . . . . 1.66 −1.00 * .F 1.35 0.76 Leu 178 A A . . . . . 1.61 −1.00 . . F 1.20 1.54 Glu 179 A A. . . . . 1.50 −1.43 . . F 0.90 1.98 Glu 180 A A . . . . . 1.89 −1.41 *. F 0.90 3.16 Lys 181 A A . . . . . 1.30 −1.91 * . F 0.90 7.66 Glu 182 AA . . . . . 1.08 −1.91 . . F 0.90 3.10 Asn 183 A A . . . . . 1.03−1.23 * * F 0.90 1.48 Lys 184 A A . . . . . 1.08 −0.59 * . F 0.75 0.55Ile 185 A A . . . . . 1.08 −0.59 * * . 0.60 0.63 Leu 186 A A . . . . .0.72 −0.59 * * . 0.60 0.68 Val 187 A A . . . . . 0.38 −0.50 . * . 0.300.49 Lys 188 A A . . . . . 0.13 −0.07 * * F 0.45 0.69 Glu 189 A . . . .T . −0.61 0.00 * * F 0.40 1.32 Thr 190 . . . . T T . −0.42 0.10 . * F0.80 1.54 Gly 191 . . . . T T . −0.50 0.24 * . F 0.65 0.67 Tyr 192 . . .. T T . 0.11 0.93 * * . 0.20 0.27 Phe 193 . . B B . . . −0.28 1.69 . . .−0.60 0.29 Phe 194 . . B B . . . −0.28 1.63 . * . −0.60 0.29 Ile 195 . .B B . . . −0.82 1.60 . . . −0.60 0.32 Tyr 196 . . B B . . . −1.29 1.49 .. . −0.60 0.28 Gly 197 . . . B T . . −1.29 1.39 . . . −0.20 0.26 Gln 198. . . B T . . −0.90 1.36 . . . −0.20 0.59 Val 199 . . . B . . C −0.201.16 . . . −0.40 0.54 Leu 200 . . . B . . C 0.73 0.40 . . . −0.10 0.92Tyr 201 . . . . T T . 0.67 −0.03 . . . 1.25 1.06 Thr 202 . . . . T T .0.77 0.06 . . F 0.80 2.06 Asp 203 . . . . T T . 0.18 0.17 . . F 0.803.91 Lys 204 A . . . . T . 0.43 −0.01 . . F 1.00 2.52 Thr 205 A A . . .. . 0.90 −0.16 . . F 0.60 1.73 Tyr 206 A A . . . . . 1.11 −0.21 . . .0.45 1.03 Ala 207 A A . . . . . 0.61 0.29 . . . −0.30 0.70 Met 208 A A .. . . . −0.28 0.97 . . . −0.60 0.40 Gly 209 A A . B . . . −0.32 1.17 * .. −0.60 0.18 His 210 A A . B . . . 0.10 0.81 * . . −0.60 0.31 Leu 211 AA . B . . . 0.39 0.31 . . . −0.30 0.61 Ile 212 A A . B . . . 1.02 −0.30. . . 0.45 1.22 Gln 213 A A . B . . . 0.77 −0.73 . * . 0.75 1.80 Arg 214A A . B . . . 1.08 −0.59 . * F 0.90 1.62 Lys 215 A A . B . . . 0.26−0.77 * * F 0.90 3.14 Lys 216 A A . B . . . 0.37 −0.81 . * F 0.90 1.35Val 217 . A B B . . . 0.91 −0.43 * * . 0.30 0.60 His 218 . A B B . . .0.91 −0.00 . * . 0.30 0.29 Val 219 . A B B . . . 0.80 −0.00 * * . 0.300.25 Phe 220 . . B B . . . −0.06 −0.00 * . . 0.30 0.57 Gly 221 A . . B .. . −0.40 0.04 . * . −0.30 0.35 Asp 222 A . . . . . . −0.36 −0.07 * . .0.50 0.63 Glu 223 A . . . . . . −1.18 −0.03 * . . 0.50 0.60 Leu 224 A .. B . . . −0.63 −0.17 . . . 0.30 0.45 Ser 225 A . . B . . . −0.74 −0.11. . . 0.30 0.39 Leu 226 A . . B . . . −1.10 0.57 . * . −0.60 0.18 Val227 A . . B . . . −0.99 1.36 . * . −0.60 0.19 Thr 228 A . . B . . .−1.66 0.67 * * . −0.60 0.28 Leu 229 A . . B . . . −1.73 0.86 * . . −0.600.18 Phe 230 A . . B . . . −1.43 0.86 * . . −0.60 0.17 Arg 231 A . . B .. . −0.62 0.61 * . . −0.60 0.21 Cys 232 . . . B T . . −0.37 0.53 * . .−0.20 0.41 Ile 233 . . . B T . . −0.27 0.46 * . . −0.20 0.46 Gln 234 . .. B T . . 0.54 0.10 * . . 0.10 0.37 Asn 235 . . . B . . C 0.93 0.10 * .. 0.05 1.19 Met 236 . . . B . . C 0.01 0.01 * . F 0.20 2.44 Pro 237 . .. B . . C 0.47 0.01 * . F 0.44 1.16 Glu 238 . . . . T . . 1.36 0.04 * .F 1.08 1.12 Thr 239 . . . . . . C 1.36 0.04 * . F 1.12 1.82 Leu 240 . .. . . . C 1.06 −0.17 * . F 1.96 1.89 Pro 241 . . . . T . . 0.99 −0.21 .. F 2.40 1.46 Asn 242 . . . . T . . 0.96 0.36 . . F 1.41 0.54 Asn 243 .. . . T T . 0.66 0.63 . . F 1.22 1.03 Ser 244 . . . . T T . 0.38 0.33 .. F 1.13 0.89 Cys 245 . . . . T T . 0.84 0.40 . . . 0.74 0.56 Tyr 246 .. . . T T . 0.17 0.43 . . . 0.20 0.35 Ser 247 A . . . . . . −0.42 0.71 .. . −0.40 0.18 Ala 248 A A . . . . . −0.38 0.83 . . . −0.60 0.34 Gly 249A A . . . . . −0.89 0.26 . . . −0.30 0.43 Ile 250 A A . . . . . −0.220.19 * . . −0.30 0.27 Ala 251 A A . . . . . 0.02 −0.20 * . . 0.30 0.46Lys 252 A A . . . . . −0.02 −0.70 . . . 0.60 0.80 Leu 253 A A . . . . .0.57 −0.70 . . F 0.90 1.13 Glu 254 A A . . . . . 0.91 −1.39 . . F 0.901.87 Glu 255 A A . . . . . 0.99 −1.89 . . F 0.90 1.62 Gly 256 A A . . .. . 1.58 −1.20 . * F 0.90 1.62 Asp 257 A A . . . . . 0.72 −1.49 . * F0.90 1.62 Glu 258 A A . . . . . 0.94 −0.80 * * F 0.75 0.77 Leu 259 A A .. . . . 0.06 −0.30 * * . 0.30 0.79 Gln 260 A A . . . . . −0.16 −0.04 * .. 0.30 0.33 Leu 261 A A . . . . . 0.30 0.39 * . . −0.30 0.30 Ala 262 A A. . . . . 0.30 0.39 * . . −0.30 0.70 Ile 263 A A . . . . . 0.30 −0.30. * . 0.30 0.70 Pro 264 A . . . . T . 0.52 −0.30 . * F 1.00 1.37 Arg 265A . . . . T . 0.52 −0.49 . * F 1.00 1.37 Glu 266 A . . . . T . 0.44−0.59 * * F 1.30 3.38 Asn 267 A . . . . T . 0.73 −0.59 * * F 1.30 1.53Ala 268 A . . . . . . 0.81 −0.63 * * . 0.95 1.05 Gln 269 A . . . . . .1.02 0.06 * * . −0.10 0.50 Ile 270 A . . . . . . 0.57 0.06 . * . 0.150.52 Ser 271 . . . . . . C 0.57 0.09 . * . 0.60 0.51 Leu 272 . . . . . .C −0.29 −0.41 . * F 1.60 0.49 Asp 273 . . . . T T . −0.01 −0.17 . * F2.25 0.52 Gly 274 . . . . T T . −0.71 −0.37 . * F 2.50 0.56 Asp 275 . .. . T T . −0.52 0.03 . * F 1.65 0.59 Val 276 A . . . . T . −0.57 0.13. * F 1.00 0.30 Thr 277 A . . B . . . −0.34 0.56 . * . −0.10 0.30 Phe278 A . . B . . . −1.16 0.63 . * . −0.35 0.18 Phe 279 A . . B . . .−0.77 1.31 . * . −0.60 0.20 Gly 280 A A . . . . . −1.58 0.67 . * . −0.600.28 Ala 281 A A . . . . . −1.53 0.87 . * . −0.60 0.27 Leu 282 A A . . .. . −1.61 0.77 * . . −0.60 0.26 Lys 283 A A . . . . . −1.30 0.41 * . .−0.60 0.33 Leu 284 A A . . . . . −0.99 0.41 . . . −0.60 0.42 Leu 285 A A. . . . . −1.03 0.34 * . . −0.30 0.65

Additional preferred nucleic acid fragments of the present inventioninclude nucleic acid molecules comprising, or alternatively, consistingof a sequence encoding one or more epitope-bearing portions ofNeutrokine-alpha. In particular, such nucleic acid fragments of thepresent invention include nucleic acid molecules comprising, oralternatively consisting of, a sequence encoding a polypeptide selectedfrom: from about Phe-115 to about Leu-147, from about Ile-150 to aboutTyr-163, from about Ser-171 to about Phe-194, from about Glu-223 toabout Tyr-246, and from about Ser-271 to about Phe-278, of the aminoacid sequence of SEQ ID NO:2. In this context, “about” means theparticularly recited ranges and ranges larger or smaller by several, afew, 5, 4, 3, 2 or 1 amino acid residues at either or both the amino-and carboxy-termini. Polypeptides encoded by these nucleic acidmolecules are also encompassed by the invention. Polypeptide fragmentswhich bear antigenic epitopes of the Neutrokine-alpha may be easilydetermined by one of skill in the art using the above-described analysisof the Jameson-Wolf antigenic index, as shown in FIG. 3. Methods fordetermining other such epitope-bearing portions of Neutrokine-alpha aredescribed in detail below.

Additional preferred nucleic acid fragments of the present inventioninclude nucleic acid molecules comprising, or alternatively consistingof a sequence encoding one or more epitope-bearing portions ofNeutrokine-alphaSV. In particular, such nucleic acid fragments of thepresent invention include nucleic acid molecules comprising, oralternatively consisting of a sequence encoding a polypeptide selectedfrom about Pro-32 to about Leu-47, from about Glu-116 to about Ser-143,from about Phe-153 to about Tyr-173, from about Pro-218 to aboutTyr-227, from about Ser-252 to about Thr-258, from about Ala-232 toabout Gln-241; from about Ile-244 to about Ala-249; and from aboutSer-252 to about Val-257, of the amino acid sequence of SEQ ID NO:19. Inthis context, “about” means the particularly recited ranges and rangeslarger or smaller by several, a few, 5, 4, 3, 2 or 1 amino acid residuesat either or both the amino- and carboxy-termini. Polypeptides encodedby these nucleic acid molecules are also encompassed by the invention.Polypeptide fragments which bear antigenic epitopes of theNeutrokine-alpha may be easily determined by one of skill in the artusing the above-described analysis of the Jameson-Wolf antigenic index.Methods for determining other such epitope-bearing portions ofNeutrokine-alphaSV are described in detail below.

In specific embodiments, the polynucleotides of the invention are lessthan 100,000 kb, 50,000 kb, 10,000 kb, 1,000 kb, 500 kb, 400 kb, 350 kb,300 kb, 250 kb, 200 kb, 175 kb, 150 kb, 125 kb, 100 kb, 75 kb, 50 kb, 40kb, 30 kb, 25 kb, 20 kb, 15 kb, 10 kb, 7.5 kb, or 5 kb in length.

In further embodiments, polynucleotides of the invention comprise atleast 15, at least 30, at least 50, at least 100, or at least 250, atleast 500, or at least 1000 contiguous nucleotides of Neutrokine-alphacoding sequence, but consist of less than or equal to 1000 kb, 500 kb,250 kb, 200 kb, 150 kb, 100 kb, 75 kb, 50 kb, 30 kb, 25 kb, 20 kb, 15kb, 10 kb, or 5 kb of genomic DNA that flanks the 5′ or 3′ codingnucleotide set forth in FIGS. 1A and 1B (SEQ ID NO:1) or FIGS. 5A and 5B(SEQ ID NO:18). In further embodiments, polynucleotides of the inventioncomprise at least 15, at least 30, at least 50, at least 100, or atleast 250, at least 500, or at least 1000 contiguous nucleotides ofNeutrokine-alpha coding sequence, but do not comprise all or a portionof any Neutrokine-alpha intron. In another embodiment, the nucleic acidcomprising Neutrokine-alpha coding sequence does not contain codingsequences of a genomic flanking gene (i.e., 5′ or 3′ to theNeutrokine-alpha gene in the genome). In other embodiments, thepolynucleotides of the invention do not contain the coding sequence ofmore than 1000, 500, 250, 100, 50, 25, 20, 15, 10, 5, 4, 3, 2, or 1genomic flanking gene(s).

In another embodiment, the invention provides an isolated nucleic acidmolecule comprising a polynucleotide which hybridizes under stringenthybridization conditions to a portion of the polynucleotide in a nucleicacid molecule of the invention described above, for instance, thesequence complementary to the coding and/or noncoding sequence depictedin FIGS. 1A and 1B (SEQ ID NO:1), the sequence of the cDNA clonecontained in the deposit having ATCC accession no. 97768, the sequencecomplementary to the coding sequence and/or noncoding sequence depictedin FIGS. 5A and 5B (SEQ ID NO:18), the sequence of the cDNA clonecontained in the deposit having ATCC accession no. 203518, the sequencecomplementary to the coding sequence and/or noncoding sequence (i.e.,transcribed, untranslated) depicted in SEQ ID NO:21, the sequencecomplementary to the coding sequence and/or noncoding sequence depictedin SEQ ID NO:22, the sequence complementary to the coding sequenceand/or noncoding sequence depicted in SEQ ID NO:27, the sequencecomplementary to the coding sequence and/or noncoding sequence depictedin SEQ ID NO:29, or fragments (such as, for example, the open readingframe or a fragment thereof) of these sequences, as described herein. By“stringent hybridization conditions” is intended overnight incubation at42° C. in a solution comprising: 50% formamide, 5×SSC (750 mM NaCl, 75mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt'ssolution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmonsperm DNA, followed by washing the filters in 0.1×SSC at about 65° C.

By a polynucleotide which hybridizes to a “portion” of a polynucleotideis intended a polynucleotide (either DNA or RNA) hybridizing to at leastabout 15 nucleotides (nt), and more preferably at least about 20 nt,still more preferably at least about 30 nt, and even more preferablyabout 30-70 (e.g., 40, 50, or 60) nucleotides, and even more preferablyabout any integer in the range of 30-70 or 80-150 nucleotides, or theentire length of the reference polynucleotide. These have uses, whichinclude, but are not limited to, diagnostic probes and primers asdiscussed above and in more detail below. By a portion of apolynucleotide of “at least about 20 nt in length,” for example, isintended to include the particularly recited ranges, larger or smallerby several (i.e. 5, 4, 3, 2, 1, or 0) amino acids, at either extreme orat both extremes of the nucleotide sequence of the referencepolynucleotide (e.g., the sequence of one or both of the depositedcDNAs, the complementary strand of the nucleotide sequence shown inFIGS. 1A and 1B (SEQ ID NO:1), the complementary strand of thenucleotide sequence shown in FIGS. 5A and 5B (SEQ ID NO:18), thecomplementary strand of the nucleotide sequence shown in SEQ ID NO:21,the complementary strand of the nucleotide sequence shown in SEQ IDNO:22, the complementary strand of the nucleotide sequence shown in SEQID NO:27 and/or the complementary strand of the nucleotide sequenceshown in SEQ ID NO:29). Of course, a polynucleotide which hybridizesonly to a poly A sequence (such as the 3′ terminal poly(A) tract of theNeutrokine-alpha cDNA shown in FIGS. 1A and 1B (SEQ ID NO:1), the 3′terminal poly(A) tract of the Neutrokine-alphaSV cDNA shown in FIGS. 5Aand 5B (SEQ ID NO:18) or the 3′ terminal poly(A) tract of theNeutrokine-alphaSV cDNA shown in SEQ ID NO:22), or to a complementarystretch of T (or U) residues, would not be included in a polynucleotideof the invention used to hybridize to a portion of a nucleic acid of theinvention, since such a polynucleotide would hybridize to any nucleicacid molecule containing a poly(A) stretch or the complement thereof(e.g., practically any double-stranded cDNA clone generated using oligodT as a primer).

As indicated, nucleic acid molecules of the present invention whichencode a Neutrokine-alpha polypeptide or a Neutrokine-alphaSVpolypeptide may include, but are not limited to, polynucleotidesencoding the amino acid sequence of the respective extracellular domainsof the polypeptides, by themselves; and the coding sequence for theextracellular domains of the respective polypeptides and additionalsequences, such as those encoding the intracellular and transmembranedomain sequences, or a pre-, or pro- or prepro-protein sequence; thecoding sequence of the respective extracellular domains of thepolypeptides, with or without the aforementioned additional codingsequences.

Also encoded by nucleic acids of the invention are the above proteinsequences together with additional, non-coding sequences, including forexample, but not limited to, introns and non-coding 5′ and 3′ sequences,such as the transcribed, non-translated sequences that play a role intranscription, mRNA processing, including splicing and polyadenylationsignals, for example, ribosome binding and stability of mRNA; anadditional coding sequence which codes for additional amino acids, suchas those which provide additional functionalities.

Thus, the sequence encoding the polypeptide may be fused to a markersequence, such as a sequence encoding a peptide which facilitatespurification of the fused polypeptide. In certain preferred embodimentsof this embodiment of the invention, the marker amino acid sequence is ahexa-histidine peptide, such as the tag provided in a pQE vector(QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311), amongothers, many of which are commercially available. As described in Gentzet al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), for instance,hexa-histidine provides for convenient purification of the fusionprotein. The “HA” tag is another peptide useful for purification whichcorresponds to an epitope derived from the influenza hemagglutininprotein, which has been described by Wilson et al., Cell 37: 767 (1984).As discussed below, other such fusion proteins include theNeutrokine-alpha or the Neutrokine-alphaSV polypeptides fused to Fc atthe N- or C-terminus.

The present invention further relates to variants of the nucleic acidmolecules of the present invention, which encode portions, analogs orderivatives of the Neutrokine-alpha or Neutrokine-alphaSV polypeptidesof SEQ ID NO:2. Variants may occur naturally, such as a natural allelicvariant. By an “allelic variant” is intended one of several alternateforms of a gene occupying a given locus on a chromosome of an organism.Genes II, Lewin, B., ed., John Wiley & Sons, New York (1985).Non-naturally occurring variants may be produced using art-knownmutagenesis techniques, which include, but are not limited tooligonucleotide mediated mutagenesis, alanine scanning, PCR mutagenesis,site directed mutagenesis (see e.g., Carter et al., Nucl. Acids Res.13:4331 (1986); and Zoller et al., Nucl. Acids Res. 10:6487 (1982)),cassette mutagenesis (see e.g., Wells et al., Gene 34:315 (1985)),restriction selection mutagenesis (see e.g., Wells, et al., Philos.Trans. R. Soc. London SerA 317:415 (1986)).

Such variants include those produced by nucleotide substitutions,deletions or additions. The substitutions, deletions or additions mayinvolve one or more nucleotides. The variants may be altered in codingregions, non-coding regions, or both. Alterations in the coding regionsmay produce conservative or non-conservative amino acid substitutions,deletions or additions. Especially preferred among these are silentsubstitutions, additions and deletions, which do not alter theproperties and activities of the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or portions thereof. Also especiallypreferred in this regard are conservative substitutions.

Additional embodiments of the invention are directed to isolated nucleicacid molecules comprising a polynucleotide which encodes the amino acidsequence of a Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide(e.g., a Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide fragmentdescribed herein) having an amino acid sequence which contains at leastone conservative amino acid substitution, but not more than 50conservative amino acid substitutions, even more preferably, not morethan 40 conservative amino acid substitutions, still more preferably,not more than 30 conservative amino acid substitutions, and still evenmore preferably, not more than 20 conservative amino acid substitutions,10-20 conservative amino acid substitutions, 5-10 conservative aminoacid substitutions, 1-5 conservative amino acid substitutions, 3-5conservative amino acid substitutions, or 1-3 conservative amino acidsubstitutions. Of course, in order of ever-increasing preference, it ishighly preferable for a polynucleotide which encodes the amino acidsequence of a Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide tohave an amino acid sequence which contains not more than 10, 9, 8, 7, 6,5, 4, 3, 2 or 1 conservative amino acid substitutions.

Further embodiments include an isolated nucleic acid moleculecomprising, or alternatively consisting of, a polynucleotide having anucleotide sequence at least 80%, 85%, or 90% identical, and morepreferably at least 95%, 96%, 97%, 98% or 99% identical to apolynucleotide selected from the group consisting of: (a) a nucleotidesequence encoding the Neutrokine-alpha polypeptide having the completeamino acid sequence in FIGS. 1A and 1B (i.e., positions 1 to 285 of SEQID NO:2); (b) a nucleotide sequence encoding the Neutrokine-alphapolypeptide having the complete amino acid sequence in SEQ ID NO:2excepting the N-terminal methionine (i.e., positions 2 to 285 of SEQ IDNO:2); (c) a fragment of the polypeptide of (b) having Neutrokine-alphafunctional activity (e.g., antigenic or biological activity); (d) anucleotide sequence encoding the predicted extracellular domain of theNeutrokine-alpha polypeptide having the amino acid sequence at positions73-285 in FIGS. 1A and 1B (SEQ ID NO:2); (e) a nucleotide sequenceencoding the Neutrokine-alpha polypeptide having the amino acid sequenceat positions 134-285 in FIGS. 1A and 1B (SEQ ID NO:2); (f) a nucleotidesequence encoding the Neutrokine-alpha polypeptide having the completeamino acid sequence encoded by the cDNA clone contained in the deposithaving ATCC accession number 97768; (g) a nucleotide sequence encodingthe extracellular domain of the Neutrokine-alpha polypeptide having theamino acid sequence encoded by the cDNA contained in the deposit havingATCC accession number 97768; and (h) a nucleotide sequence complementaryto any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g),or (h) above. The present invention also encompasses the abovepolynucleotide sequences fused to a heterologous polynucleotidesequence. Polypeptides encoded by these polynucleotides and nucleic acidmolecules are also encompassed by the invention.

Highly preferred embodiments of the invention are directed to nucleicacid molecules comprising, or alternatively consisting of apolynucleotide having a nucleotide sequence at least 80%, 85%, 90%identical and more preferably at least 95%, 96%, 97%, 98%, 99% or 100%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). Preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 90%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). More preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 95%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). More preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 96%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2).

Additionally, more preferred embodiments of the invention are directedto nucleic acid molecules comprising, or alternatively consisting of apolynucleotide having a nucleotide sequence at least 97% to apolynucleotide sequence encoding the Neutrokine-alpha polypeptide havingthe amino acid sequence at positions 134-285 in FIGS. 1A and 1B (SEQ IDNO:2). Additionally, more preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 98%to a polynucleotide sequence encoding the Neutrokine-alpha polypeptidehaving the amino acid sequence at positions 134-285 in FIGS. 1A and 1B(SEQ ID NO:2). Additionally, more preferred embodiments of the inventionare directed to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 99%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2).

A further embodiment of the invention relates to an isolated nucleicacid molecule comprising a polynucleotide which encodes the amino acidsequence of a Neutrokine-alphaSV polypeptide (e.g., a Neutrokine-alphaSVpolypeptide fragment described herein) having an amino acid sequencewhich contains at least one conservative amino acid substitution, butnot more than 50 conservative amino acid substitutions, even morepreferably, not more than 40 conservative amino acid substitutions,still more preferably not more than 30 conservative amino acidsubstitutions, and still even more preferably not more than 20conservative amino acid substitutions. Of course, in order ofever-increasing preference, it is highly preferable for a polynucleotidewhich encodes the amino acid sequence of a Neutrokine-alpha polypeptideto have an amino acid sequence which contains not more than 7-10, 5-10,3-7, 3-5, 2-5, 1-5, 1-3, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 conservativeamino acid substitutions.

Further embodiments include an isolated nucleic acid moleculecomprising, or alternatively, consisting of a polynucleotide having anucleotide sequence at least 80%, 85% or 90% identical, and morepreferably at least 95%, 96%, 97%, 98% or 99% identical to apolynucleotide selected from the group consisting of: (a) a nucleotidesequence encoding the Neutrokine-alphaSV polypeptide having the completeamino acid sequence in FIGS. 5A and 5B (i.e., positions 1 to 266 of SEQID NO:19); (b) a nucleotide sequence encoding the Neutrokine-alphaSVpolypeptide having the complete amino acid sequence in SEQ ID NO:19excepting the N-terminal methionine (i.e., positions 2 to 266 of SEQ IDNO:2); (c) a nucleotide sequence encoding the predicted extracellulardomain of the Neutrokine-alphaSV polypeptide having the amino acidsequence at positions 73-285 in FIGS. 5A and 5B (SEQ ID NO:19); (d) anucleotide sequence encoding the Neutrokine-alphaSV polypeptide havingthe complete amino acid sequence encoded by the cDNA clone contained inthe deposit having ATCC accession number 203518; (e) a nucleotidesequence encoding the extracellular domain of the Neutrokine-alphaSVpolypeptide having the amino acid sequence encoded by the cDNA clonecontained in the deposit having ATCC accession number 203518; and (f) anucleotide sequence complementary to any of the nucleotide sequences in(a), (b), (c), (d) or (e), above.

Further, the invention includes a polynucleotide comprising, oralternatively, consisting of, a sequence at least 90%, or at least 95%,identical to any portion of at least about 10 contiguous nucleotides,about 20 contiguous nucleotides, about 25 contiguous nucleotides, orabout 30 contiguous nucleotides, preferably at least about 40nucleotides, or at least about 50 nucleotides, of the sequence fromnucleotide 1 to nucleotide 1082 in FIGS. 1A and 1B (SEQ ID NO:1),preferably excluding the nucleotide sequences determined from theabove-listed 4 cDNA clones and the nucleotide sequences from nucleotide797 to 1082, 810 to 1082, and 346 to 542. The invention also includes apolynucleotide comprising, or alternatively consisting of, a sequence atleast 90%, or at least 95%, identical to any portion of at least about10 contiguous nucleotides, about 20 contiguous nucleotides, about 25contiguous nucleotides, or about 30 contiguous nucleotides, preferablyat least about 40 nucleotides, or at least about 50 nucleotides, of thesequence in FIGS. 5A and 5B (SEQ ID NO:18), preferably excluding thenucleotide sequences determined from the above-listed 4 cDNA clones. Theinvention also includes a polynucleotide comprising, or alternativelyconsisting of a sequence at least 90%, or at least 95%, identical to anyportion of at least about 10 contiguous nucleotides, about 20 contiguousnucleotides, about 25 contiguous nucleotides, or about 30 contiguousnucleotides, preferably at least about 40 nucleotides, or at least about50 nucleotides, of the sequence in SEQ ID NO:21, preferably excludingthe nucleotide sequences determined from the above-listed 4 cDNA clones.The invention also includes a polynucleotide comprising a sequence atleast 90%, or at least 95%, identical to any portion of at least about10 contiguous nucleotides, about 20 contiguous nucleotides, about 25contiguous nucleotides, or about 30 contiguous nucleotides, preferablyat least about 40 nucleotides, or at least about 50 nucleotides, of thesequence in SEQ ID NO:22, preferably excluding the nucleotide sequencesdetermined from the above-listed 4 cDNA clones. The invention alsoincludes a polynucleotide comprising a sequence at least 90%, or atleast 95%, identical to any portion of at least about 10 contiguousnucleotides, about 20 contiguous nucleotides, about 25 contiguousnucleotides, or about 30 contiguous nucleotides, preferably at leastabout 40 nucleotides, or at least about 50 nucleotides, of the sequencein SEQ ID NO:27, preferably excluding the nucleotide sequencesdetermined from the above-listed 4 cDNA clones. The invention alsoincludes a polynucleotide comprising a sequence at least 90%, or atleast 95%, identical to any portion of at least about 10 contiguousnucleotides, about 20 contiguous nucleotides, about 25 contiguousnucleotides, or about 30 contiguous nucleotides, preferably at leastabout 40 nucleotides, or at least about 50 nucleotides, of the sequencein SEQ ID NO:29, preferably excluding the nucleotide sequencesdetermined from the above-listed 4 cDNA clones. In this context “about”includes the particularly recited ranges, larger or smaller by several(i.e. 5, 4, 3, 2 or 1) amino acids, at either extreme or at bothextremes.

By a polynucleotide having a nucleotide sequence at least, for example,95% “identical” to a reference nucleotide sequence encoding aNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide is intended thatthe nucleotide sequence of the polynucleotide is identical to thereference sequence except that the polynucleotide sequence may includeup to five mismatches per each 100 nucleotides of the referencenucleotide sequence encoding the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide. In other words, to obtain apolynucleotide having a nucleotide sequence at least 95% identical to areference nucleotide sequence, up to 5% of the nucleotides in thereference sequence may be deleted or substituted with anothernucleotide, or a number of nucleotides up to 5% of the total nucleotidesin the reference sequence may be inserted into the reference sequence.These mutations of the reference sequence may occur at the 5′ or 3′terminal positions of the reference nucleotide sequence or anywherebetween those terminal positions, interspersed either individually amongnucleotides in the reference sequence or in one or more contiguousgroups within the reference sequence. The reference (query) sequence maybe the entire nucleotide sequence encoding Neutrokine-alpha orNeutrokine-alphaSV, as shown in FIGS. 1A and 1B (SEQ ID NO:1) and FIGS.5A and 5B (SEQ ID NO:18), respectively, or any Neutrokine-alpha such as,for example, the Neutrokine-alpha polynucleotides shown as SEQ IDNOs:21, 22, 27 or 28, or any Neutrokine-alpha or Neutrokine-alphaSVpolynucleotide fragment as described herein.

As a practical matter, whether any particular nucleic acid molecule isat least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to, forinstance, the nucleotide sequences shown in FIGS. 1A and 1B, or thenucleotide sequences shown in FIGS. 5A and 5B, or to the nucleotidessequence of the deposited cDNA clones, or to any Neutrokine-alphapolynucleotide such as, for example, the Neutrokine-alphapolynucleotides shown as SEQ ID NOs:21, 22, 27 or 28, or fragmentsthereof, can be determined conventionally using known computer programssuch as the Bestfit program (Wisconsin Sequence Analysis Package,Version 8 for Unix, Genetics Computer Group, University Research Park,575 Science Drive, Madison, Wis. 53711). Bestfit uses the local homologyalgorithm of Smith and Waterman to find the best segment of homologybetween two sequences (Advances in Applied Mathematics 2:482-489(1981)). When using Bestfit or any other sequence alignment program todetermine whether a particular sequence is, for instance, 95% identicalto a reference sequence according to the present invention, theparameters are set, of course, such that the percentage of identity iscalculated over the full length of the reference nucleotide sequence andthat gaps in homology of up to 5% of the total number of nucleotides inthe reference sequence are allowed.

In a specific embodiment, the identity between a reference (query)sequence (a sequence of the present invention) and a subject sequence,also referred to as a global sequence alignment, is determined using theFASTDB computer program based on the algorithm of Brutlag and colleagues(Comp. App. Biosci. 6:237-245 (1990)). In a sequence alignment the queryand subject sequences are both DNA sequences. An RNA sequence can becompared by converting U's to T's. The result of said global sequencealignment is in percent identity. Preferred parameters used in a FASTDBalignment of DNA sequences to calculate percent identity are:Matrix=Unitary, k-tuple=4, Mismatch Penalty=1, Joining Penalty=30,Randomization Group Length=0, Cutoff Score=1, Gap Penalty=5, Gap SizePenalty 0.05, Window Size=500 or the length of the subject nucleotidesequence, whichever is shorter. According to this embodiment, if thesubject sequence is shorter than the query sequence because of 5′ or 3′deletions, not because of internal deletions, a manual correction ismade to the results to take into consideration the fact that the FASTDBprogram does not account for 5′ and 3′ truncations of the subjectsequence when calculating percent identity. For subject sequencestruncated at the 5′ or 3′ ends, relative to the query sequence, thepercent identity is corrected by calculating the number of bases of thequery sequence that are 5′ and 3′ of the subject sequence, which are notmatched/aligned, as a percent of the total bases of the query sequence.A determination of whether a nucleotide is matched/aligned is determinedby results of the FASTDB sequence alignment. This percentage is thensubtracted from the percent identity, calculated by the above FASTDBprogram using the specified parameters, to arrive at a final percentidentity score. This corrected score is what is used for the purposes ofthis embodiment. Only bases outside the 5′ and 3′ bases of the subjectsequence, as displayed by the FASTDB alignment, which are notmatched/aligned with the query sequence, are calculated for the purposesof manually adjusting the percent identity score. For example, a 90 basesubject sequence is aligned to a 100 base query sequence to determinepercent identity. The deletions occur at the 5′ end of the subjectsequence and therefore, the FASTDB alignment does not show amatched/alignment of the first 10 bases at 5′ end. The 10 unpaired basesrepresent 10% of the sequence (number of bases at the 5′ and 3′ ends notmatched/total number of bases in the query sequence) so 10% issubtracted from the percent identity score calculated by the FASTDBprogram. If the remaining 90 bases were perfectly matched the finalpercent identity would be 90%. In another example, a 90 base subjectsequence is compared with a 100 base query sequence. This time thedeletions are internal deletions so that there are no bases on the 5′ or3′ of the subject sequence which are not matched/aligned with the query.In this case the percent identity calculated by FASTDB is not manuallycorrected. Once again, only bases 5′ and 3′ of the subject sequencewhich are not matched/aligned with the query sequence are manuallycorrected for. No other manual corrections are made for the purposes ofthis embodiment.

The present application is directed to nucleic acid molecules at least80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to the nucleicacid sequences (i.e., polynucleotides) disclosed herein (e.g., thosedisclosed in FIGS. 1A and 1B (SEQ ID NO:1) or to the nucleic acidsequence of the deposited cDNAs), irrespective of whether they encode apolypeptide having Neutrokine-alpha and/or Neutrokine-alphaSV functionalactivity (e.g., biological activity). In addition, the presentapplication is also directed to nucleic acid molecules at least 80%,85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to the nucleic acidsequence shown in FIGS. 5A and 5B (SEQ ID NO:18) or to the nucleic acidsequence of the deposited cDNA, irrespective of whether they encode apolypeptide having Neutrokine-alphaSV activity. Moreover, the presentapplication is also directed to nucleic acid molecules at least 80%,85%, 90%, 92%, 95%, 96%, 97%, 98%, 99% identical to the nucleic acidsequence shown in SEQ ID NOs:21, 22, 27 or 28, irrespective of whetherthey encode a polypeptide having Neutrokine-alpha activity. This isbecause even where a particular nucleic acid molecule does not encode apolypeptide having Neutrokine-alpha and/or Neutrokine-alphaSV activity,one of skill in the art would still know how to use the nucleic acidmolecule, for instance, as a hybridization probe or a polymerase chainreaction (PCR) primer. Uses of the nucleic acid molecules of the presentinvention that do not encode a polypeptide having Neutrokine-alphaand/or Neutrokine-alphaSV activity include, inter alia, (1) isolatingthe Neutrokine-alpha and/or Neutrokine-alphaSV gene or allelic variantsthereof in a cDNA library; (2) in situ hybridization (e.g., “FISH”) tometaphase chromosomal spreads to provide precise chromosomal location ofthe Neutrokine-alpha and/or Neutrokine-alphaSV gene, as described inVerma et al., Human Chromosomes: A Manual of Basic Techniques, PergamonPress, New York (1988); and Northern Blot analysis for detectingNeutrokine-alpha and/or Neutrokine-alphaSV mRNA expression in specifictissues.

Preferred, however, are nucleic acid molecules having sequences at least80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to the nucleicacid sequences disclosed herein (e.g., the nucleotide sequence shown inFIGS. 1A and 1B (SEQ ID NO:1) and the nucleic acid sequence of thedeposited cDNAs, or fragments thereof), which do, in fact, encode apolypeptide having Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide functional activity (e.g., biological activity). Alsopreferred are nucleic acid molecules having sequences at least 80%, 85%,90%, 92%, 95%, 96%, 97%, 98% or 99% identical to the nucleic acidsequence shown in FIGS. 5A and 5B (SEQ ID NO:18) or to the nucleic acidsequence of the deposited cDNA which do, in fact, encode a polypeptidehaving Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide functionalactivity (e.g., biological activity). Also preferred are nucleic acidmolecules having sequences at least 80%, 85%, 90%, 92%, 95%, 96%, 97%,98% or 99% identical to the nucleic acid sequence shown SEQ ID NOs:21,22, 27 or 28 which do, in fact, encode a polypeptide havingNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide functionalactivity (e.g., biological activity).

By “a polypeptide having Neutrokine-alpha polypeptide functionalactivity” (e.g., biological activity) and “a polypeptide havingNeutrokine-alphaSV polypeptide functional activity” (e.g., biologicalactivity) are intended polypeptides exhibiting activity similar, but notnecessarily identical, to an activity of the extracellular domain or thefull-length Neutrokine-alpha or Neutrokine-alphaSV polypeptides of theinvention, as measured in a particular functional assay (e.g.,immunological or biological assay). For example, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide functional activity can be measured bythe ability of a polypeptide sequence described herein to form multimers(e.g., homodimers and homotrimers) with the complete Neutrokine-alphaand/or Neutrokine-alphaSV or extracellular domain of Neutrokine-alphaand/or Neutrokine-alphaSV, and to bind a Neutrokine-alpha and/orNeutrokine-alphaSV ligand Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide functional activity can be also be measured by determiningthe ability of a polypeptide of the invention to induce lymphocyte(e.g., B cell) proliferation, differentiation or activation and/or toextend B cell survival. These functional assays can be routinelyperformed using techniques described herein (e.g., see Example 6) andotherwise known in the art. Additionally, Neutrokine-alpha orNeutrokine-alphaSV polypeptides of the present invention modulate cellproliferation, cytotoxicity, cell survival and cell death. An in vitrocell proliferation, cytotoxicity, cell survival, and cell death assayfor measuring the effect of a protein on certain cells can be performedby using reagents well known and commonly available in the art fordetecting cell replication and/or death. For instance, numerous suchassays for TNF-related protein activities are described in the variousreferences in this disclosure. Briefly, an example of such an assayinvolves collecting human or animal (e.g., mouse) cells and mixing with(1) transfected host cell-supernatant containing Neutrokine-alphaprotein (or a candidate polypeptide) or (2) nontransfected hostcell-supernatant control, and measuring the effect on cell numbers orviability after incubation of certain period of time. Such cellproliferation and/or survival modulation activities as can be measure inthis type of assay are useful for treating tumor, tumor metastasis,infections, autoimmune diseases, inflammation and other immune-relateddiseases.

Neutrokine-alpha modulates cell proliferation and differentiation in adose-dependent manner in the above-described assay. Accordingly, it ispreferred that “a polypeptide having Neutrokine-alpha polypeptidefunctional activity” (e.g., biological activity) includes polypeptidesthat also exhibit any of the same cell modulatory (particularlyimmunomodulatory) activities in the above-described assays in adose-dependent manner. Although the degree of dose-dependent activityneed not be identical to that of the Neutrokine-alpha polypeptides,preferably, “a polypeptide having Neutrokine-alpha polypeptidefunctional activity” will exhibit substantially similar dose-dependencein a given activity as compared to the Neutrokine-alpha polypeptides(i.e., the candidate polypeptide will exhibit greater activity or notmore than about 25-fold less and, preferably, not more than abouttenfold less activity relative to the reference Neutrokine-alphapolypeptides).

In certain preferred embodiments, “a polypeptide having Neutrokine-alphapolypeptide functional activity” (e.g., biological activity) and “apolypeptide having Neutrokine-alphaSV polypeptide functional activity”(e.g., biological activity) includes polypeptides that also exhibit anyof the same B cell (or other cell type) modulatory (particularlyimmunomodulatory) activities described in FIGS. 8A, 8B, 9A, 9B, 10A,10B, 10C, 10D, 10E, 10F, 10G, 11A, 11B, and 11C and in Example 6.

Like other members of TNF family, Neutrokine-alpha exhibits activity onleukocytes including, for example, monocytes, lymphocytes (e.g., Bcells) and neutrophils. For this reason Neutrokine-alpha is active indirecting the proliferation, differentiation and migration of these celltypes. Such activity is useful for immune enhancement or suppression,myeloprotection, stem cell mobilization, acute and chronic inflammatorycontrol and treatment of leukemia. Assays for measuring such activityare known in the art. For example, see Peters et al., Immun. Today17:273 (1996); Young et al., J. Exp. Med. 182:1111 (1995); Caux et al.,Nature 390:258 (1992); and Santiago-Schwarz et al., Adv. Exp. Med. Biol.378:7 (1995).

Of course, due to the degeneracy of the genetic code, one of ordinaryskill in the art will immediately recognize that a large number of thenucleic acid molecules having a sequence at least 80%, 85%, 90%, 92%,95%, 96%, 97%, 98%, or 99% identical to the nucleic acid sequencecontained in cDNA clone deposited in ATCC accession no. 97768, or thenucleic acid sequence shown in FIGS. 1A and 1B (SEQ ID NO:1), orfragments thereof, will encode a polypeptide “having Neutrokine-alphapolypeptide functional activity” (e.g., biological activity). One ofordinary skill in the art will also immediately recognize that a largenumber of the nucleic acid molecules having a sequence at least 80%,85%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% identical to the nucleic acidsequence contained in cDNA clone deposited in ATCC accession no. 203518or the nucleic acid sequence shown in FIGS. 5A and 5B (SEQ ID NO:18)will encode a polypeptide “having Neutrokine-alphaSV polypeptidefunctional activity” (e.g., biological activity). In fact, sincedegenerate variants of these nucleotide sequences all encode the samepolypeptide, this will be clear to the skilled artisan even withoutperforming the above described comparison assay. It will be furtherrecognized in the art that, for such nucleic acid molecules that are notdegenerate variants, a reasonable number will also encode a polypeptidehaving Neutrokine-alpha and/or Neutrokine-alphaSV activity. This isbecause the skilled artisan is fully aware of amino acid substitutionsthat are either less likely or not likely to significantly effectprotein function (e.g., replacing one aliphatic amino acid with a secondaliphatic amino acid), as further described below.

Similarly, polynucleotides encoding polypeptides which contain all orsome portion of the region V-142 through K-160 of SEQ ID NO:2 are likelyto be valuable diagnostic and therapeutic polynucleotides with regard todetecting and/or altering expression of either Neutrokine-alpha orNeutrokine-alphaSV polynucleotides. In addition, polynucleotides whichspan the junction of amino acid residues T-141 and G-142 of theNeutrokine-alphaSV polypeptide shown in SEQ ID NO:19 (in between whichthe V-142 through K-160 amino acid sequence of Neutrokine-alpha isapparently inserted), are also likely to be useful both diagnosticallyand therapeutically. Such T-141/G-142 spanning polynucleotides willexhibit a much higher likelihood of hybridization withNeutrokine-alphaSV polynucleotides than with Neutrokine-alphapolynucleotides. A partial, non-limiting, non-exclusive list of suchNeutrokine-alphaSV polypeptides which are encoded by polynucleotides ofthe invention includes polypeptides comprising, or alternativelyconsisting of, an amino acid sequence selected from the following: G-121through E-163; E-122 through E-163; G-123 through E-163; N-124 throughE-163; S-125 through E-163; S-126 through E-163; Q-127 through E-163;N-128 through E-163; S-129 through E-163; R-130 through E-163; N-131through E-163; K-132 through E-163; R-133 through E-163; A-134 throughE-163; V-135 through E-163; Q-136 through E-163; G-137 through E-163;P-138 through E-163; E-139 through E-163; E-140 through E-163; T-141through E-163; G-142 through E-163; S-143 through E-163; Y-144 throughE-163; T-145 through E-163; F-146 through E-163; V-147 through E-163;P-148 through E-163; W-149 through E-163; L-150 through E-163; L-151through E-163; S-152 through E-163; F-153 through E-163; K-154 throughE-163; R-155 through E-163; G-156 through E-163; S-157 through E-163;A-158 through E-163; L-159 through E-163; E-160 through E-163; E-161through E-163; K-162 through E-163; G-121 through K-162; G-121 throughE-161; G-121 through E-160; G-121 through L-159; G-121 through A-158;G-121 through S-157; G-121 through G-156; G-121 through R-155; G-121through K-154; G-121 through F-153; G-121 through S-152; G-121 throughL-151; G-121 through L-150; G-121 through W-149; G-121 through P-148;G-121 through V-147; G-121 through F-146; G-121 through T-145; G-121through Y-144; G-121 through S-143; G-121 through G-142; G-121 throughT-141; G-121 through E-140; G-121 through E-139; G-121 through P-138;G-121 through G-137; G-121 through Q-136; G-121 through V-135; G-121through A-134; G-121 through R-133; G-121 through K-132; G-121 throughN-131; G-121 through R-130; G-121 through S-129; G-121 through N-128;G-121 through Q-127; G-121 through S-126; G-121 through S-125; G-121through N-124; G-121 through G-123; and G-121 through E-122 of SEQ IDNO:19. Polypeptides encoded by these polynucleotides are alsoencompassed by the invention.

Vectors and Host Cells

The present invention also relates to vectors which include the isolatedDNA molecules of the present invention, host cells which are geneticallyengineered with the recombinant vectors, or which are otherwiseengineered to produce the polypeptides of the invention, and theproduction of Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides,or fragments thereof, by recombinant or synthetic techniques.

In one embodiment, the polynucleotides of the invention are joined to avector (e.g., a cloning or expression vector). The vector may be, forexample, a phage, plasmid, viral or retroviral vector. Retroviralvectors may be replication competent or replication defective. In thelatter case, viral propagation generally will occur only incomplementing host cells. The polynucleotides may be joined to a vectorcontaining a selectable marker for propagation in a host. Introductionof the vector construct into the host cell can be effected by techniquesknown in the art which include, but are not limited to, calciumphosphate transfection, DEAE-dextran mediated transfection, cationiclipid-mediated transfection, electroporation, transduction, infection orother methods. Such methods are described in many standard laboratorymanuals, such as Davis et al., Basic Methods In Molecular Biology(1986).

Generally, recombinant expression vectors will include origins ofreplication and selectable markers permitting transformation of the hostcell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiaeTRP1 gene, and a promoter derived from a highly-expressed gene to directtranscription of a downstream structural sequence. Such promoters can bederived from operons encoding glycolytic enzymes such as3-phosphoglycerate kinase (PGK), a-factor, acid phosphatase, or heatshock proteins, among others. The heterologous structural sequence isassembled in appropriate phase with translation initiation andtermination sequences, and preferably, a leader sequence capable ofdirecting secretion of translated protein into the periplasmic space orextracellular medium. Optionally, the heterologous sequence can encode afusion protein including an N-terminal identification peptide impartingdesired characteristics, for example, stabilization or simplifiedpurification of expressed recombinant product.

In one embodiment, the DNA of the invention is operatively associatedwith an appropriate heterologous regulatory element (e.g., promoter orenhancer), such as, the phage lambda PL promoter, the E. coli lac, trp,phoA, and tac promoters, the SV40 early and late promoters and promotersof retroviral LTRs, to name a few. Other suitable promoters will beknown to the skilled artisan.

As indicated, the expression vectors will preferably include at leastone selectable marker. Such markers include dihydrofolate reductase,G418 or neomycin resistance for eukaryotic cell culture andtetracycline, kanamycin or ampicillin resistance genes for culturing inE. coli and other bacteria. Representative examples of appropriate hostsinclude, but are not limited to, bacterial cells, such as E. coli,Streptomyces and Salmonella typhimurium cells; fungal cells, such asyeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCCAccession No. 201178)); insect cells such as Drosophila S2 andSpodoptera Sf9 cells; animal cells such as CHO, COS, 293 and Bowesmelanoma cells; and plant cells. Appropriate culture mediums andconditions for the above-described host cells are known in the art.

The host cell can be a higher eukaryotic cell, such as a mammalian cell(e.g., a human derived cell), or a lower eukaryotic cell, such as ayeast cell, or the host cell can be a prokaryotic cell, such as abacterial cell. The host strain may be chosen which modulates theexpression of the inserted gene sequences, or modifies and processes thegene product in the specific fashion desired. Expression from certainpromoters can be elevated in the presence of certain inducers; thusexpression of the genetically engineered polypeptide may be controlled.Furthermore, different host cells have characteristics and specificmechanisms for the translational and post-translational processing andmodification (e.g., phosphorylation, cleavage) of proteins. Appropriatecell lines can be chosen to ensure the desired modifications andprocessing of the foreign protein expressed. Selection of appropriatevectors and promoters for expression in a host cell is a well-knownprocedure and the requisite techniques for expression vectorconstruction, introduction of the vector into the host and expression inthe host are routine skills in the art.

Useful expression vectors for bacterial use are constructed by insertinga structural DNA sequence encoding a desired protein together withsuitable translation initiation and termination signals in operablereading phase with a functional promoter. The vector will comprise oneor more phenotypic selectable markers and an origin of replication toensure maintenance of the vector and to, if desirable, provideamplification within the host. Suitable prokaryotic hosts fortransformation include E. coli, Bacillus subtilis, Salmonellatyphimurium, and various species within the genera Pseudomonas,Streptomyces, and Staphylococcus, although others may also be employedas a matter of choice. As a representative, but nonlimiting example,useful expression vectors for bacterial use can comprise a selectablemarker and bacterial origin of replication derived from commerciallyavailable plasmids comprising genetic elements of the well-known cloningvector pBR322 (ATCC 37017). Such commercial vectors include, forexample, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM1(Promega Biotec, Madison, Wis., USA). These pBR322 “backbone” sectionsare combined with an appropriate promoter and the structural sequence tobe expressed. Among vectors preferred for use in bacteria include pHE4-5(ATCC Accession No. 209311; and variations thereof), pQE70, pQE60 andpQE-9, available from QIAGEN, Inc., supra; pBS vectors, Phagescriptvectors, Bluescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, availablefrom Stratagene; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5available from Pharmacia. Preferred expression vectors for use in yeastsystems include, but are not limited to, pYES2, pYD1, pTEF1/Zeo,pYES2/GS, pPICZ, pGAPZ, pGAPZalpha, pPIC9, pPIC3.5, pHIL-D2, pHIL-S1,pPIC3.5K, pPIC9K, and PA0815 (all available from Invitrogen, Carlsbad,Calif.). Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44,pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL(available from Pharmacia). Other suitable vectors will be readilyapparent to the skilled artisan.

Following transformation of a suitable host strain and growth of thehost strain to an appropriate cell density, the selected promoter isinduced by appropriate means (e.g., temperature shift or chemicalinduction) and cells are cultured for an additional period. Cells aretypically harvested by centrifugation, disrupted by physical or chemicalmeans, and the resulting crude extract retained for furtherpurification.

Microbial cells employed in expression of proteins can be disrupted byany convenient method, including freeze-thaw cycling, sonication,mechanical disruption, or use of cell lysing agents, such methods arewell know to those skilled in the art.

In one embodiment, the yeast Pichia pastoris is used to expressNeutrokine-alpha protein in a eukaryotic system. Pichia pastoris is amethylotrophic yeast which can metabolize methanol as its sole carbonsource. A main step in the methanol metabolization pathway is theoxidation of methanol to formaldehyde using O₂. This reaction iscatalyzed by the enzyme alcohol oxidase. In order to metabolize methanolas its sole carbon source, Pichia pastoris must generate high levels ofalcohol oxidase due, in part, to the relatively low affinity of alcoholoxidase for O₂. Consequently, in a growth medium depending on methanolas a main carbon source, the promoter region of one of the two alcoholoxidase genes (AOX1) is highly active. In the presence of methanol,alcohol oxidase produced from the AOX1 gene comprises up toapproximately 30% of the total soluble protein in Pichia pastoris. See,Ellis, S. B., et al., Mol. Cell. Biol. 5:1111-21 (1985); Koutz, P. J, etal., Yeast 5:167-77 (1989); Tschopp, J. F., et al., Nucl. Acids Res.15:3859-76 (1987). Thus, a heterologous coding sequence, such as, forexample, a Neutrokine-alpha or Neutrokine-alphaSV polynucleotide of thepresent invention, under the transcriptional regulation of all or partof the AOX1 regulatory sequence is expressed at exceptionally highlevels in Pichia yeast grown in the presence of methanol.

In one example, the plasmid vector pPIC9K is used to express DNAencoding a Neutrokine-alpha or Neutrokine-alphaSV polypeptide of theinvention, as set forth herein, in a Pichia yeast system essentially asdescribed in “Pichia Protocols: Methods in Molecular Biology,” D. R.Higgins and J. Cregg, eds. The Humana Press, Totowa, N.J., 1998. Thisexpression vector allows expression and secretion of a Neutrokine-alphaor Neutrokine-alphaSV protein of the invention by virtue of the strongAOX1 promoter linked to the Pichia pastoris alkaline phosphatase (PHO)secretory signal peptide (i.e., leader) located upstream of a multiplecloning site.

Many other yeast vectors could be used in place of pPIC9K, such as,pYES2, pYD1, pTEF1/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalpha, pPIC9,pPIC3.5, pHIL-D2, pHIL-S1, pPIC3.5K, and PA0815, as one skilled in theart would readily appreciate, as long as the proposed expressionconstruct provides appropriately located signals for transcription,translation, secretion (if desired), and the like, including an in-frameAUG as required.

In one embodiment, high-level expression of a heterologous codingsequence, such as, for example, a Neutrokine-alpha or Neutrokine-alphaSVpolynucleotide of the present invention, may be achieved by cloning theheterologous polynucleotide of the invention into an expression vectorsuch as, for example, pGAPZ or pGAPZalpha, and growing the yeast culturein the absence of methanol.

Transcription of the DNA encoding the polypeptides of the presentinvention by higher eukaryotes is increased by inserting an enhancersequence into the vector. Enhancers are cis-acting elements of DNA,usually about from 10 to 300 by that act on a promoter to increase itstranscription. Examples including the SV40 enhancer on the late side ofthe replication origin by 100 to 270, a cytomegalovirus early promoterenhancer, the polyoma enhancer on the late side of the replicationorigin, and adenovirus enhancers.

Various mammalian cell culture systems can also be employed to expressrecombinant protein. Examples of mammalian expression systems includethe COS-7 lines of monkey kidney fibroblasts, described by Gluzman (Cell23:175 (1981)), and other cell lines capable of expressing a compatiblevector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines.Mammalian expression vectors will comprise an origin of replication, asuitable promoter and enhancer, and also any necessary ribosome bindingsites, polyadenylation site, splice donor and acceptor sites,transcriptional termination sequences, and 5′ flanking nontranscribedsequences. DNA sequences derived from the SV40 splice, andpolyadenylation sites may be used to provide the required nontranscribedgenetic elements.

In a specific embodiment, constructs designed to express a portion ofthe extracellular domain of the Neutrokine-alpha (e.g., amino acidresidues Ala-134 through Leu-285) are preferred. One of skill in the artwould be able to use the polynucleotide and polypeptide sequencesprovided as SEQ ID NO:1 and SEQ ID NO:2, respectively, or SEQ ID NO:18and SEQ ID NO:19, respectively, to design polynucleotide primers togenerate such an expression construct.

In another embodiment, constructs designed to express the entirepredicted extracellular domain of the Neutrokine-alpha (i.e., amino acidresidues Gln-73 through Leu-285) are preferred. One of skill in the artwould be able to use the polynucleotide and polypeptide sequencesprovided as SEQ ID NO:1 and SEQ ID NO:2, respectively, or SEQ ID NO:18and SEQ ID NO:19, respectively, to design polynucleotide primers togenerate such an expression construct.

In addition to encompassing host cells containing the vector constructsdiscussed herein, the invention also encompasses primary, secondary, andimmortalized host cells of vertebrate origin, particularly mammalianorigin, that have been engineered to delete or replace endogenousgenetic material (e.g., Neutrokine-alpha coding sequence), and/or toinclude genetic material (e.g., heterologous polynucleotide sequences)that is operably associated with Neutrokine-alpha polynucleotides of theinvention, and which activates, alters, and/or amplifies endogenousNeutrokine-alpha polynucleotides. For example, techniques known in theart may be used to operably associate heterologous control regions(e.g., promoter and/or enhancer) and endogenous Neutrokine-alphapolynucleotide sequences via homologous recombination (see, e.g., U.S.Pat. No. 5,641,670, issued Jun. 24, 1997; International Publication No.WO 96/29411, published Sep. 26, 1996; International Publication No. WO94/12650, published Aug. 4, 1994; Koller et al., Proc. Natl. Acad. Sci.USA 86:8932-8935 (1989); and Zijlstra et al., Nature 342:435-438 (1989),the disclosures of each of which are incorporated by reference in theirentireties).

The host cells described infra can be used in a conventional manner toproduce the gene product encoded by the recombinant sequence.Alternatively, cell-free translation systems can also be employed toproduce the polypeptides of the invention using RNAs derived from theDNA constructs of the present invention.

The polypeptide of the invention may be expressed or synthesized in amodified form, such as a fusion protein (comprising the polypeptidejoined via a peptide bond to a heterologous protein sequence (of adifferent protein)), and may include not only secretion signals, butalso additional heterologous functional regions. Such a fusion proteincan be made by ligating polynucleotides of the invention and the desirednucleic acid sequence encoding the desired amino acid sequence to eachother, by methods known in the art, in the proper reading frame, andexpressing the fusion protein product by methods known in the art.Alternatively, such a fusion protein can be made by protein synthetictechniques, e.g., by use of a peptide synthesizer. Thus, for instance, aregion of additional amino acids, particularly charged amino acids, maybe added to the N-terminus of the polypeptide to improve stability andpersistence in the host cell, during purification, or during subsequenthandling and storage. Also, peptide moieties may be added to thepolypeptide to facilitate purification. Such regions may be removedprior to final preparation of the polypeptide. The addition of peptidemoieties to polypeptides to engender secretion or excretion, to improvestability and to facilitate purification, among others, are familiar androutine techniques in the art.

In one embodiment, polynucleotides encoding Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention may be fused to thepelB pectate lyase signal sequence to increase the efficiency toexpression and purification of such polypeptides in Gram-negativebacteria. See, U.S. Pat. Nos. 5,576,195 and 5,846,818, the contents ofwhich are herein incorporated by reference in their entireties.

A preferred fusion protein comprises a heterologous region fromimmunoglobulin that is useful to stabilize and purify proteins. Forexample, EP-A-0 464 533 (Canadian counterpart 2045869) discloses fusionproteins comprising various portions of constant region ofimmunoglobulin molecules together with another human protein or partthereof. In many cases, the Fc part in a fusion protein is thoroughlyadvantageous for use in therapy and diagnosis and thus results, forexample, in improved pharmacokinetic properties (EP-A 0232 262). On theother hand, for some uses it would be desirable to be able to delete theFc part after the fusion protein has been expressed, detected andpurified in the advantageous manner described. This is the case when Fcportion proves to be a hindrance to use in therapy and diagnosis, forexample when the fusion protein is to be used as antigen forimmunizations. In drug discovery, for example, human proteins, such ashIL-5 has been fused with Fc portions for the purpose of high-throughputscreening assays to identify antagonists of hIL-5. See, D. Bennett etal., J. Molecular Recognition 8:52-58 (1995) and K. Johanson et al., J.Biol. Chem. 270:9459-9471 (1995).

Polypeptides of the present invention include naturally purifiedproducts, products of chemical synthetic procedures, and productsproduced by recombinant techniques from a prokaryotic or eukaryotichost, including, for example, bacterial, yeast, higher plant, insect andmammalian cells. Depending upon the host employed in a recombinantproduction procedure, the polypeptides of the present invention may beglycosylated or may be non-glycosylated. In addition, polypeptides ofthe invention may also include an initial modified methionine residue,in some cases as a result of host-mediated processes.

Polypeptides of the invention can be chemically synthesized usingtechniques known in the art (e.g., see Creighton, 1983, Proteins:Structures and Molecular Principles, W.H. Freeman & Co., N.Y., andHunkapiller, M., et al., 1984, Nature 310:105-111). For example, apeptide corresponding to a fragment of the complete Neutrokine-alpha orNeutrokine-alphaSV polypeptides of the invention can be synthesized byuse of a peptide synthesizer. Furthermore, if desired, nonclassicalamino acids or chemical amino acid analogs can be introduced as asubstitution or addition into the Neutrokine-alpha or Neutrokine-alphaSVpolynucleotide sequence. Non-classical amino acids include, but are notlimited to, to the D-isomers of the common amino acids,2,4-diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid,Abu, 2-amino butyric acid, g-Abu, e-Ahx, 6-amino hexanoic acid, Aib,2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine,norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline,cysteic acid, t-butylglycine, t-butylalanine, phenylglycine,cyclohexylalanine, b-alanine, fluoro-amino acids, designer amino acidssuch as b-methyl amino acids, Ca-methyl amino acids, Na-methyl aminoacids, and amino acid analogs in general. Furthermore, the amino acidcan be D (dextrorotary) or L (levorotary).

The invention encompasses Neutrokine-alpha or Neutrokine-alphaSVpolypeptides which are differentially modified during or aftertranslation, e.g., by glycosylation, acetylation, phosphorylation,amidation, derivatization by known protecting/blocking groups,proteolytic cleavage, linkage to an antibody molecule or other cellularligand, etc. Any of numerous chemical modifications may be carried outby known techniques, including but not limited, to specific chemicalcleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8protease, NaBH₄, acetylation, formylation, oxidation, reduction,metabolic synthesis in the presence of tunicamycin, etc.

Additional post-translational modifications encompassed by the inventioninclude, for example, e.g., N-linked or O-linked carbohydrate chains,processing of N-terminal or C-terminal ends), attachment of chemicalmoieties to the amino acid backbone, chemical modifications of N-linkedor O-linked carbohydrate chains, and addition or deletion of anN-terminal methionine residue as a result of procaryotic host cellexpression. The polypeptides may also be modified with a detectablelabel, such as an enzymatic, fluorescent, isotopic or affinity label toallow for detection and isolation of the protein. In addition,polypeptides of the invention may be modified by iodination.

In one embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the invention may also be labeled with biotin. In otherrelated embodiments, biotinylated Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention may be used, forexample, as an imaging agent or as a means of identifying one or moreNeutrokine-alpha and/or Neutrokine-alphaSV receptor(s) or othercoreceptor or coligand molecules.

Also provided by the invention are chemically modified derivatives ofNeutrokine-alpha or Neutrokine-alphaSV which may provide additionaladvantages such as increased solubility, stability and in vivo or invitro circulating time of the polypeptide, or decreased immunogenicity(see U.S. Pat. No. 4,179,337). The chemical moieties for derivitizationmay be selected from water soluble polymers such as polyethylene glycol,ethylene glycol/propylene glycol copolymers, carboxymethylcellulose,dextran, polyvinyl alcohol and the like. The polypeptides may bemodified at random positions within the molecule, or at predeterminedpositions within the molecule and may include one, two, three or moreattached chemical moieties.

The polymer may be of any molecular weight, and may be branched orunbranched. For polyethylene glycol, the preferred molecular weight isbetween about 1 kDa and about 100 kDa (the term “about” indicating thatin preparations of polyethylene glycol, some molecules will weigh more,some less, than the stated molecular weight) for ease in handling andmanufacturing. Other sizes may be used, depending on the desiredtherapeutic profile (e.g., the duration of sustained release desired,the effects, if any on biological activity, the ease in handling, thedegree or lack of antigenicity and other known effects of thepolyethylene glycol to a therapeutic protein or analog). For example,the polyethylene glycol may have an average molecular weight of about200, 500, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500,6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10,000, 10,500, 11,000,11,500, 12,000, 12,500, 13,000, 13,500, 14,000, 14,500, 15,000, 15,500,16,000, 16,500, 17,000, 17,500, 18,000, 18,500, 19,000, 19,500, 20,000,25,000, 30,000, 35,000, 40,000, 50,000, 55,000, 60,000, 65,000, 70,000,75,000, 80,000, 85,000, 90,000, 95,000, or 100,000 kDa.

As noted above, the polyethylene glycol may have a branched structure.Branched polyethylene glycols are described, for example, in U.S. Pat.No. 5,643,575; Morpurgo et al., Appl. Biochem. Biotechnol. 56:59-72(1996); Vorobjev et al., Nucleosides Nucleotides 18:2745-2750 (1999);and Caliceti et al., Bioconjug. Chem. 10:638-646 (1999), the disclosuresof each of which are incorporated herein by reference.

The polyethylene glycol molecules (or other chemical moieties) should beattached to the protein with consideration of effects on functional orantigenic domains of the protein. There are a number of attachmentmethods available to those skilled in the art, e.g., EP 0 401 384,herein incorporated by reference (coupling PEG to G-CSF), see also Maliket al., Exp. Hematol. 20:1028-1035 (1992) (reporting pegylation ofGM-CSF using tresyl chloride). For example, polyethylene glycol may becovalently bound through amino acid residues via a reactive group, suchas, a free amino or carboxyl group. Reactive groups are those to whichan activated polyethylene glycol molecule may be bound. The amino acidresidues having a free amino group may include, for example, lysineresidues and the N-terminal amino acid residues; those having a freecarboxyl group may include aspartic acid residues, glutamic acidresidues, and the C-terminal amino acid residue. Sulfhydryl groups mayalso be used as a reactive group for attaching the polyethylene glycolmolecules. Preferred for therapeutic purposes is attachment at an aminogroup, such as attachment at the N-terminus or lysine group.

As suggested above, polyethylene glycol may be attached to proteins vialinkage to any of a number of amino acid residues. For example,polyethylene glycol can be linked to a proteins via covalent bonds tolysine, histidine, aspartic acid, glutamic acid, or cysteine residues.One or more reaction chemistries may be employed to attach polyethyleneglycol to specific amino acid residues (e.g., lysine, histidine,aspartic acid, glutamic acid, or cysteine) of the protein or to morethan one type of amino acid residue (e.g., lysine, histidine, asparticacid, glutamic acid, cysteine and combinations thereof) of the protein.

One may specifically desire proteins chemically modified at theN-terminus. Using polyethylene glycol as an illustration, one may selectfrom a variety of polyethylene glycol molecules (by molecular weight,branching, etc.), the proportion of polyethylene glycol molecules toprotein (or peptide) molecules in the reaction mix, the type ofpegylation reaction to be performed, and the method of obtaining theselected N-terminally pegylated protein. The method of obtaining theN-terminally pegylated preparation (i.e., separating this moiety fromother monopegylated moieties if necessary) may be by purification of theN-terminally pegylated material from a population of pegylated proteinmolecules. Selective proteins chemically modified at the N-terminusmodification may be accomplished by reductive alkylation which exploitsdifferential reactivity of different types of primary amino groups(lysine versus the N-terminal) available for derivatization in aparticular protein. Under the appropriate reaction conditions,substantially selective derivatization of the protein at the N-terminuswith a carbonyl group containing polymer is achieved.

As indicated above, pegylation of the proteins of the invention may beaccomplished by any number of means. For example, polyethylene glycolmay be attached to the protein either directly or by an interveninglinker. Linkerless systems for attaching polyethylene glycol to proteinsare described in Delgado et al., Crit. Rev. Thera. Drug Carrier Sys.9:249-304 (1992); Francis et al., Intern. J. of Hematol. 68:1-18 (1998);U.S. Pat. No. 4,002,531; U.S. Pat. No. 5,349,052; WO 95/06058; and WO98/32466, the disclosures of each of which are incorporated herein byreference.

One system for attaching polyethylene glycol directly to amino acidresidues of proteins without an intervening linker employs tresylatedMPEG, which is produced by the modification of monmethoxy polyethyleneglycol (MPEG) using tresylchloride (ClSO₂CH₂CF₃). Upon reaction ofprotein with tresylated MPEG, polyethylene glycol is directly attachedto amine groups of the protein. Thus, the invention includesprotein-polyethylene glycol conjugates produced by reacting proteins ofthe invention with a polyethylene glycol molecule having a2,2,2-trifluoreothane sulphonyl group.

Polyethylene glycol can also be attached to proteins using a number ofdifferent intervening linkers. For example, U.S. Pat. No. 5,612,460, theentire disclosure of which is incorporated herein by reference,discloses urethane linkers for connecting polyethylene glycol toproteins. Protein-polyethylene glycol conjugates wherein thepolyethylene glycol is attached to the protein by a linker can also beproduced by reaction of proteins with compounds such asMPEG-succinimidylsuccinate, MPEG activated with1,1′-carbonyldiimidazole, MPEG-2,4,5-trichloropenylcarbonate,MPEG-p-nitrophenolcarbonate, and various MPEG-succinate derivatives. Anumber additional polyethylene glycol derivatives and reactionchemistries for attaching polyethylene glycol to proteins are describedin WO 98/32466, the entire disclosure of which is incorporated herein byreference. Pegylated protein products produced using the reactionchemistries set out herein are included within the scope of theinvention.

The number of polyethylene glycol moieties attached to each protein ofthe invention (i.e., the degree of substitution) may also vary. Forexample, the pegylated proteins of the invention may be linked, onaverage, to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20, or morepolyethylene glycol molecules. Similarly, the average degree ofsubstitution within ranges such as 1-3, 2-4, 3-5, 4-6, 5-7, 6-8, 7-9,8-10, 9-11, 10-12, 11-13, 12-14, 13-15, 14-16, 15-17, 16-18, 17-19, or18-20 polyethylene glycol moieties per protein molecule. Methods fordetermining the degree of substitution are discussed, for example, inDelgado et al., Crit. Rev. Thera. Drug Carrier Sys. 9:249-304 (1992).

The Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides can berecovered and purified by known methods which include, but are notlimited to, ammonium sulfate or ethanol precipitation, acid extraction,anion or cation exchange chromatography, phosphocellulosechromatography, hydrophobic interaction chromatography, affinitychromatography, hydroxylapatite chromatography and lectinchromatography. Most preferably, high performance liquid chromatography(“HPLC”) is employed for purification.

Neutrokine-Alpha Polypeptides

The Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides of theinvention may be in monomers or multimers (i.e., dimers, trimers,tetramers and higher multimers). Accordingly, the present inventionrelates to monomers and multimers of the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention, their preparation, andcompositions (preferably, pharmaceutical compositions) containing them.In specific embodiments, the polypeptides of the invention are monomers,dimers, trimers or tetramers. In additional embodiments, the multimersof the invention are at least dimers, at least trimers, or at leasttetramers.

Multimers encompassed by the invention may be homomers or heteromers. Asused herein, the term homomer, refers to a multimer containing onlyNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides of the invention(including Neutrokine-alpha and/or Neutrokine-alphaSV fragments,variants, and fusion proteins, as described herein). These homomers maycontain Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides havingidentical or different amino acid sequences. In a specific embodiment, ahomomer of the invention is a multimer containing only Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides having an identical amino acidsequence. In another specific embodiment, a homomer of the invention isa multimer containing Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides having different amino acid sequences. In specificembodiments, the multimer of the invention is a homodimer (e.g.,containing Neutrokine-alpha and/or Neutrokine-alphaSV polypeptideshaving identical or different amino acid sequences) or a homotrimer(e.g., containing Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides having identical or different amino acid sequences). In apreferred embodiment, the multimer of the invention is a homotrimer. Inadditional embodiments, the homomeric multimer of the invention is atleast a homodimer, at least a homotrimer, or at least a homotetramer.

As used herein, the term heteromer refers to a multimer containingheterologous polypeptides (i.e., polypeptides of a different protein) inaddition to the Neutrokine-alpha and/or Neutrokine-alphaSV polypeptidesof the invention. In a specific embodiment, the multimer of theinvention is a heterodimer, a heterotrimer, or a heterotetramer. Inadditional embodiments, the heteromeric multimer of the invention is atleast a heterodimer, at least a heterotrimer, or at least aheterotetramer. In a further nonexclusive embodiment, the heteromers ofthe invention contain CD40 ligand polypeptide sequence(s), orbiologically active fragment(s) or variant(s) thereof.

Multimers of the invention may be the result of hydrophobic,hydrophilic, ionic and/or covalent associations and/or may be indirectlylinked, by for example, liposome formation. Thus, in one embodiment,multimers of the invention, such as, for example, homodimers orhomotrimers, are formed when polypeptides of the invention contact oneanother in solution. In another embodiment, heteromultimers of theinvention, such as, for example, heterotrimers or heterotetramers, areformed when polypeptides of the invention contact antibodies to thepolypeptides of the invention (including antibodies to the heterologouspolypeptide sequence in a fusion protein of the invention) in solution.In other embodiments, multimers of the invention are formed by covalentassociations with and/or between the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention. Such covalentassociations may involve one or more amino acid residues contained inthe polypeptide sequence (e.g., that recited in SEQ ID NO:2 or SEQ IDNO:19, or contained in the polypeptide encoded by the clones depositedin connection with this application). In one instance, the covalentassociations are cross-linking between cysteine residues located withinthe polypeptide sequences which interact in the native (i.e., naturallyoccurring) polypeptide. In another instance, the covalent associationsare the consequence of chemical or recombinant manipulation.Alternatively, such covalent associations may involve one or more aminoacid residues contained in the heterologous polypeptide sequence in aNeutrokine-alpha and/or Neutrokine-alphaSV fusion protein. In oneexample, covalent associations are between the heterologous sequencecontained in a fusion protein of the invention (see, e.g., U.S. Pat. No.5,478,925). In a specific example, the covalent associations are betweenthe heterologous sequence contained in a Neutrokine-alpha-Fc and/orNeutrokine-alphaSV-Fc fusion protein of the invention (as describedherein). In another specific example, covalent associations of fusionproteins of the invention are between heterologous polypeptide sequencefrom another TNF family ligand/receptor member that is capable offorming covalently associated multimers, such as for example,oseteoprotegerin (see, e.g., International Publication No. WO 98/49305,the contents of which are herein incorporated by reference in itsentirety). In another specific example, covalent associations of fusionproteins of the invention are between heterologous polypeptide sequencefrom CD40L, or a soluble fragment thereof. In another embodiment, two ormore Neutrokine-alpha and/or Neutrokine-alpha polypeptides of theinvention are joined through synthetic linkers (e.g., peptide,carbohydrate or soluble polymer linkers). Examples include those peptidelinkers described in U.S. Pat. No. 5,073,627 (hereby incorporated byreference). Proteins comprising multiple Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides separated by peptide linkers may beproduced using conventional recombinant DNA technology.

Another method for preparing multimer Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention involves use ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides fused to aleucine zipper or isoleucine zipper polypeptide sequence. Leucine zipperor isoleucine zipper domains are polypeptides that promotemultimerization of the proteins in which they are found. Leucine zipperswere originally identified in several DNA-binding proteins (Landschulzet al., Science 240:1759, (1988)), and have since been found in avariety of different proteins. Among the known leucine zippers orisoleucine zippers are naturally occurring peptides and derivativesthereof that dimerize or trimerize. Examples of leucine zipper domainssuitable for producing soluble multimeric Neutrokine-alpha and/orNeutrokine-alphaSV proteins are those described in PCT application WO94/10308, hereby incorporated by reference. Recombinant fusion proteinscomprising a soluble Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide fused to a peptide that dimerizes or trimerizes in solutionare expressed in suitable host cells, and the resulting solublemultimeric Neutrokine-alpha and/or Neutrokine-alphaSV is recovered fromthe culture supernatant using techniques known in the art.

Certain members of the TNF family of proteins are believed to exist intrimeric form (Beutler and Huffel, Science 264:667, 1994; Banner et al.,Cell 73:431, 1993). Thus, trimeric Neutrokine-alpha and/orNeutrokine-alphaSV may offer the advantage of enhanced biologicalactivity. Preferred leucine zipper moieties are those thatpreferentially form trimers. One example is a leucine zipper derivedfrom lung surfactant protein D (SPD), as described in Hoppe et al. (FEBSLetters 344:191, (1994)) and in U.S. patent application Ser. No.08/446,922, hereby incorporated by reference. Other peptides derivedfrom naturally occurring trimeric proteins may be employed in preparingtrimeric Neutrokine-alpha and/or Neutrokine-alphaSV.

In another example, proteins of the invention are associated byinteractions between the Flag® polypeptide sequence contained inFlag®-Neutrokine alpha or Flag®-Neutrokine-alphaSV fusion proteins ofthe invention. In a further embodiment, proteins of the invention areassociated by interactions between the heterologous polypeptide sequencecontained in Flag®-Neutrokine-alpha or Flag®-Neutrokine-alphaSV fusionproteins of the invention and anti-Flag® antibody.

The multimers of the invention may be generated using chemicaltechniques known in the art. For example, polypeptides desired to becontained in the multimers of the invention may be chemicallycross-linked using linker molecules and linker molecule lengthoptimization techniques known in the art (see, e.g., U.S. Pat. No.5,478,925, which is herein incorporated by reference in its entirety).Additionally, multimers of the invention may be generated usingtechniques known in the art to form one or more inter-moleculecross-links between the cysteine residues located within the sequence ofthe polypeptides desired to be contained in the multimer (see, e.g.,U.S. Pat. No. 5,478,925, which is herein incorporated by reference inits entirety). Further, polypeptides of the invention may be routinelymodified by the addition of cysteine or biotin to the C terminus orN-terminus of the polypeptide and techniques known in the art may beapplied to generate multimers containing one or more of these modifiedpolypeptides (see, e.g., U.S. Pat. No. 5,478,925, which is hereinincorporated by reference in its entirety). Additionally, techniquesknown in the art may be applied to generate liposomes containing thepolypeptide components desired to be contained in the multimer of theinvention (see, e.g., U.S. Pat. No. 5,478,925, which is hereinincorporated by reference in its entirety).

Alternatively, multimers of the invention may be generated using geneticengineering techniques known in the art. In one embodiment, polypeptidescontained in multimers of the invention are produced recombinantly usingfusion protein technology described herein or otherwise known in the art(see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated byreference in its entirety). In a specific embodiment, polynucleotidescoding for a homodimer of the invention are generated by ligating apolynucleotide sequence encoding a polypeptide of the invention to asequence encoding a linker polypeptide and then further to a syntheticpolynucleotide encoding the translated product of the polypeptide in thereverse orientation from the original C-terminus to the N-terminus(lacking the leader sequence) (see, e.g., U.S. Pat. No. 5,478,925, whichis herein incorporated by reference in its entirety). In anotherembodiment, recombinant techniques described herein or otherwise knownin the art are applied to generate recombinant polypeptides of theinvention which contain a transmembrane domain and which can beincorporated by membrane reconstitution techniques into liposomes (see,e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by referencein its entirety).

In one embodiment, the invention provides an isolated Neutrokine-alphapolypeptide having the amino acid sequence encoded by the cDNA clonecontained in ATCC No. 97768, or the amino acid sequence in FIGS. 1A and1B (SEQ ID NO:2), or a polypeptide comprising a portion (i.e., afragment) of the above polypeptides. In another embodiment, theinvention provides an isolated Neutrokine-alphaSV polypeptide having theamino acid encoded by the cDNA clone contained in ATCC No. 203518, orthe amino acid sequence in FIGS. 5A and 5B (SEQ ID NO:19), or apolypeptide comprising a portion (i.e., fragment) of the abovepolypeptides.

Polypeptide fragments of the present invention include polypeptidescomprising or alternatively, consisting of, an amino acid sequencecontained in SEQ ID NO:2, encoded by the cDNA contained in the plasmidhaving ATCC accession number 97768, or encoded by nucleic acids whichhybridize (e.g., under stringent hybridization conditions) to thenucleotide sequence contained in the deposited clone, or thecomplementary strand of the nucleotide sequence shown in FIGS. 1A-B (SEQID NO:1.

Additionally, polypeptide fragments of the present invention includepolypeptides comprising or alternatively, consisting of, an amino acidsequence contained in SEQ ID NO:19, encoded by the cDNA contained in theplasmid having ATCC accession number 203518, or encoded by nucleic acidswhich hybridize (e.g., under stringent hybridization conditions) to thenucleotide sequence contained in the deposited clone, or thecomplementary strand of the nucleotide sequence shown in FIGS. 5A-B (SEQID NO:18).

Additionally, polypeptide fragments of the present invention includepolypeptides comprising or alternatively, consisting of, an amino acidsequence encoded by nucleic acids which hybridize (e.g., underhybridization conditions described herein) to the complementary strandof the nucleotide sequence shown in SEQ ID NO:21.

Polypeptide fragments of the present invention also include polypeptidescomprising or alternatively, consisting of, an amino acid sequencecontained in SEQ ID NO:23, or encoded by nucleic acids which hybridize(e.g., under hybridization conditions described herein) to thecomplementary strand of the nucleotide sequence shown in SEQ ID NO:22.

In addition, polypeptide fragments of the present invention includepolypeptides comprising or alternatively, consisting of, an amino acidsequence contained in SEQ ID NO:28, or encoded by nucleic acids whichhybridize (e.g., under hybridization conditions described herein) to thecomplementary strand of the nucleotide sequence shown in SEQ ID NO:27.

Additionally, polypeptide fragments of the present invention includepolypeptides comprising or alternatively, consisting of, an amino acidsequence contained in SEQ ID NO:30, or encoded by nucleic acids whichhybridize (e.g., under hybridization conditions described herein) to thecomplementary strand of the nucleotide sequence shown in SEQ ID NO:29.

Polypeptide fragments of the present invention include polypeptidescomprising or alternatively, consisting of, an amino acid sequencecontained in SEQ ID NO:2, encoded by the cDNA contained in the depositedclone, or encoded by nucleic acids which hybridize (e.g., understringent hybridization conditions) to the nucleotide sequence containedin the deposited clone, or shown in FIGS. 1A and 1B (SEQ ID NO:1) or thecomplementary strand thereto. Protein fragments may be “free-standing,”or comprised within a larger polypeptide of which the fragment forms apart or region, most preferably as a single continuous region.Representative examples of polypeptide fragments of the invention,include, for example, fragments that comprise or alternatively, consistof from about amino acid residues: 1 to 50, 51 to 100, 101 to 150, 151to 200, 201 to 250, and/or 251 to 285 of SEQ ID NO:2. Moreover,polypeptide fragments can be at least 10, 20, 30, 40, 50, 60, 70, 80,90, 100, 110, 120, 130, 140, 150, 175 or 200 amino acids in length.

In specific embodiments, polypeptide fragments of the inventioncomprise, or alternatively consist of, amino acid residues: 1-46, 31-44,47-72, 73-285, 73-83, 94-102, 148-152, 166-181, 185-209, 210-221,226-237, 244-249, 253-265, and/or 277-284, as depicted in FIGS. 1A and1B (SEQ ID NO:2). Polynucleotides encoding these polypeptides are alsoencompassed by the invention.

It will be recognized by one of ordinary skill in the art that mutationstargeted to regions of a Neutrokine-alpha polypeptide of the inventionwhich encompass the nineteen amino acid residue insertion which is notfound in the Neutrokine-alphaSV polypeptide sequence (i.e., amino acidresidues Val-142 through Lys-160 of the sequence presented in FIGS. 1Aand 1B and in SEQ ID NO:2) may affect the observed biological activitiesof the Neutrokine-alpha polypeptide. More specifically, a partial,non-limiting and non-exclusive list of such residues of theNeutrokine-alpha polypeptide sequence which may be targeted for mutationincludes the following amino acid residues of the Neutrokine-alphapolypeptide sequence as shown in SEQ ID NO:2: V-142; T-143; Q-144;D-145; C-146; L-147; Q-148; L-149; I-150; A-151; D-152; S-153; E-154;T-155; P-156; T-157; I-158; Q-159; and K-160. Polynucleotides encodingNeutrokine-alpha polypeptides which have one or more mutations in theregion from V-142 through K-160 of SEQ ID NO:2 are contemplated.Polypeptides encoded by these polynucleotides are also encompassed bythe invention.

Polypeptide fragments may be “free-standing,” or comprised within alarger polypeptide of which the fragment forms a part or region, mostpreferably as a single continuous region. Representative examples ofpolypeptide fragments of the invention, include, for example, fragmentsthat comprise or alternatively, consist of from about amino acidresidues: 1 to 15, 16-30, 31-46, 47-55, 56-72, 73-104, 105-163, 163-188,186-210 and 210-284 of the amino acid sequence disclosed in SEQ ID NO:2.Additional representative examples of polypeptide fragments of theinvention, include, for example, fragments that comprise oralternatively, consist of from about amino acid residues: 1 to 143,1-150, 47-143, 47-150, 73-143, 73-150, 100-150, 140-145, 142-148,140-150, 140-200, 140-225, and 140-266 of the amino acid sequencedisclosed in SEQ ID NO:19. Moreover, polypeptide fragments can be atleast 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150,175 or 200 amino acids in length. In this context, “about” means theparticularly recited ranges and ranges larger or smaller by several, afew, 5, 4, 3, 2 or 1 amino acid residues at either or both the amino-and carboxy-termini. Polynucleotides encoding these polypeptidefragments are also encompassed by the invention.

Additional preferred embodiments encompass polypeptide fragmentscomprising, or alternatively consisting of, the predicted intracellulardomain of Neutrokine-alpha (amino acid residues 1-46 of SEQ ID NO:2),the predicted transmembrane domain of Neutrokine-alpha (amino acidresidues 47-72 of SEQ ID NO:2), the predicted extracellular domain ofNeutrokine-alpha (amino acid residues 73-285 of SEQ ID NO:2), thepredicted TNF conserved domain of Neutrokine-alpha (amino acids 191 to284 of SEQ ID NO:2), and a polypeptide comprising, or alternatively,consisting of the predicted intracellular domain fused to the predictedextracellular domain of Neutrokine-alpha (amino acid residues 1-46 fusedto amino acid residues 73-285 of SEQ ID NO:2). Polynucleotides encodingthese polypeptides are also encompassed by the invention.

Further additional preferred embodiments encompass polypeptide fragmentscomprising, or alternatively consisting of, the predicted intracellulardomain of Neutrokine-alphaSV (amino acid residues 1-46 of SEQ ID NO:19),the predicted transmembrane domain of Neutrokine-alphaSV (amino acidresidues 47-72 of SEQ ID NO:19), the predicted extracellular domain ofNeutrokine-alphaSV (amino acid residues 73-266 of SEQ ID NO:19), thepredicted TNF conserved domain of Neutrokine-alphaSV (amino acids 172 to265 of SEQ ID NO:19), and a polypeptide comprising, or alternatively,consisting of the predicted intracellular domain fused to the predictedextracellular domain of Neutrokine-alphaSV (amino acid residues 1-46fused to amino acid residues 73-266 of SEQ ID NO:19). Polynucleotidesencoding these polypeptides are also encompassed by the invention.

Certain additional embodiments of the invention encompass polypeptidefragments comprising, or alternatively consisting of, the predictedbeta-pleated sheet regions identified in FIGS. 7A-1 and 7A-2. Thesepolypeptide fragments of the invention comprise, or alternativelyconsist of, amino acid residues Gln-144 to Ala-151, Phe-172 to Lys-173,Ala-177 to Glu-179, Asn-183 to Ile-185, Gly-191 to Lys-204, His-210 toVal-219, Leu-226 to Pro-237, Asn-242 to Ala-251, Gly-256 to Ile-263and/or Val-276 to Leu-284 of SEQ ID NO:2. In another, nonexclusiveembodiment, these polypeptide fragments of the invention also comprise,or alternatively consist of, amino acid residues Phe-153 to Lys-154,Ala-158 to Glu-160, Asn-164 to Ile-166, Gly-172 to Lys-185, His-191 toVal-200, Leu-207 to Pro-218, Asn-223 to Ala-232, Gly-237 to Ile-244and/or Val-257 to Leu-265 of SEQ ID NO:19; and amino acid residuesPhe-42 to Lys-43, Ala-47 to Glu-49, Asn-53 to Ile-55, Gly-61 to Pro-74,His-80 to Val-89, Leu-96 to Pro-107, Asn-112 to Ala-121, Gly-126 toIle-133 and/or Asp-146 to Leu-154 of SEQ ID NO:23. In furthernonexclusive embodiments, these polypeptide fragments of the inventionalso comprise, or alternatively consist of, amino acid residues Gln-78to Ala-85; Phe-106 to Lys-107, Ala-111 to Glu-113, Asn-117 to Ile-119,Gly-125 to Lys-138, His-144 to Val-153, Leu-160 to Pro-171, Asn-176 toAla-185, Gly-190 to Ile-197 and/or Val-210 to Leu-218 of SEQ ID NO:28;and amino acid residues Gln-78 to Ala-85; Phe-106 to Lys-107, Ala-111 toGlu-113, Asn-117 to Ile-119, Gly-125 to Lys-138, His-144 to Val-153,Leu-160 to Pro-171, Asn-176 to Ala-185, Gly-190 to Ile-197 and/orVal-210 to Leu-218 of SEQ ID NO:30. Polynucleotides encoding thesepolypeptide fragments are also provided.

A partial, non-limiting, and exemplary list of polypeptides of theinvention which comprise, or alternatively consist of, combinations ofamino acid sequences of the invention includes, for example, [Met-1 toLys-113] fused to [Leu-114 to Thr-141] fused to [Ile-142 to Lys-160]fused to [Gly-161 to Gln-198] fused to [Val-199 to Ala-248] fused to[Gly-250 to Leu-285] of SEQ ID NO:2; [Met-1 to Lys-113] fused to[Ile-142 to Lys-160] fused to [Gly-161 to Gln-198] fused to [Val-199 toAla-248] fused to [Gly-250 to Leu-285] of SEQ ID NO:2; or [Met-1 toLys-113] fused to [Leu-114 to Thr-141] fused to [Ile-142 to Lys-160]fused to [Gly-161 to Gln-198] fused to [Gly-250 to Leu-285] of SEQ IDNO:2. Other combinations may include the polypeptide fragments in anorder other than that recited above (e.g., [Leu-114 to Thr-141] fused to[Val-199 to Ala-248] fused to [Gly-250 to Leu-285] fused to [Ile-142 toLys-160] of SEQ ID NO:2). Other combinations may also includeheterologous polypeptide fragments as described herein and/or otherpolypeptides or polypeptide fragments of the present invention (e.g.,[Met-1 to Lys-113] fused to [Leu-114 to Thr-141] fused to [Ile-142 toLys-160] fused to [Gly-161 to Gln-198] fused to [Gly-250 to Leu-285] ofSEQ ID NO:2 fused to a FLAG tag). Polynucleotides encoding any of thesepolypeptides are encompassed by the invention.

An additional partial, non-limiting, and exemplary list of polypeptidesof the invention which comprise, or alternatively consist of,combinations of amino acid sequences includes, for example, [Met-1 toLys-113] fused to [Leu-114 to Thr-141] fused to [Gly-142 to Gln-179]fused to [Val-180 to Ala-229] fused to [Gly-230 to Leu-266] of SEQ IDNO:19; [Met-1 to Lys-113] fused to [Gly-142 to Gln-179] fused to[Val-180 to Ala-229] fused to [Gly-230 to Leu-266] of SEQ ID NO:19; or[Met-1 to Lys-113] fused to [Leu-114 to Thr-141] fused to [Gly-142 toGln-179] fused to [Gly-230 to Leu-266] of SEQ ID NO:19. Othercombinations may include the polypeptide fragments in an order otherthan that recited above (e.g., [Leu-114 to Thr-141] fused to [Val-180 toAla-229] fused to [Gly-230 to Leu-266] fused to [Gly-142 to Gln-179] ofSEQ ID NO:19). Other combinations may also include heterologouspolypeptide fragments as described herein and/or other polypeptides orpolypeptide fragments of the present invention (e.g., [Met-1 to Lys-113]fused to [Leu-114 to Thr-141] fused to [Gly-142 to Gln-179] fused to[Gly-230 to Leu-266] of SEQ ID NO:19 fused to a FLAG tag).Polynucleotides encoding any of these polypeptides are encompassed bythe invention.

A further partial, non-limiting, and exemplary list of polypeptides ofthe invention which comprise, or alternatively consist of, combinationsof amino acid sequences includes, for example, [Met-1 to Lys-106] fusedto [Leu-107 to Thr-134] fused to [Ile-167 to Lys-184] fused to [Gly-185to Gln-224] fused to [Val-225 to Ala-272] fused to [Gly-273 to Leu-309]of SEQ ID NO:23; [Met-1 to Lys-106] fused to [Glu-135 to Asn-165] fusedto [Ile-167 to Lys-184] fused to [Gly-185 to Gln-224] fused to [Val-225to Ala-272] fused to [Gly-273 to Leu-309] of SEQ ID NO:23; or [Met-1 toLys-106] fused to [Leu-107 to Thr-134] fused to [Glu-135 to Asn-165]fused to [Ile-167 to Lys-184] fused to [Gly-185 to Gln-224] fused to[Gly-273 to Leu-309] of SEQ ID NO:23. Other combinations may include thepolypeptide fragments in an order other than that recited above (e.g.,[Met-1 to Lys-106] fused to [Gly-185 to Gln-224] fused to [Ile-167 toLys-184] fused to [Val-225 to Ala-272] fused to [Leu-107 to Thr-134]fused to [Gly-273 to Leu-309] of SEQ ID NO:23). Other combinations mayalso include heterologous polypeptide fragments as described hereinand/or other polypeptides or polypeptide fragments of the presentinvention (e.g., [Met-1 to Lys-106] fused to [Glu-135 to Asn-165] fusedto [Ile-167 to Lys-184] fused to [Gly-185 to Gln-224] fused to [Val-225to Ala-272] fused to [Gly-273 to Leu-309] of SEQ ID NO:23 fused to aFLAG tag). Polynucleotides encoding any of these polypeptides areencompassed by the invention.

A further partial, non-limiting, and exemplary list of polypeptides ofthe invention which comprise, or alternatively consist of, combinationsof amino acid sequences includes, for example, [Tyr-1 to Lys-47] fusedto [Leu-48 to Thr-75] fused to [Ile-76 to Lys-94] fused to [Gly-95 toGln-132] fused to [Val-133 to Ala-182] fused to [Gly-183 to Ala-219] ofSEQ ID NO:28; [Tyr-1 to Lys-47] fused to [Leu-48 to Thr-75] fused to[Ile-76 to Lys-94] fused to [Val-133 to Ala-182] of SEQ ID NO:28; or[Tyr-1 to Lys-47] fused to [Ile-76 to Lys-94] fused to [Val-133 toAla-182] fused to [Gly-183 to Ala-219] of SEQ ID NO:28. Othercombinations may include the polypeptide fragments in an order otherthan that recited above (e.g., [Tyr-1 to Lys-47] fused to [Gly-183 toAla-219] fused to [Val-133 to Ala-182] fused to [Leu-48 to Thr-75] ofSEQ ID NO:28). Other combinations may also include heterologouspolypeptide fragments as described herein and/or other polypeptides orpolypeptide fragments of the present invention (e.g., [Leu-48 to Thr-75]fused to [Ile-76 to Lys-94] fused to [Gly-95 to Gln-132] fused to[Val-133 to Ala-182] of SEQ ID NO:28 fused to an Fc receptor tag).Polynucleotides encoding any of these polypeptides are encompassed bythe invention.

A further partial, non-limiting, and exemplary list of polypeptides ofthe invention which comprise, or alternatively consist of, combinationsof amino acid sequences includes, for example, [Tyr-1 to Lys-47] fusedto [Leu-48 to Thr-75] fused to [Ile-76 to Lys-94] fused to [Gly-95 toGln-132] fused to [Val-133 to Ala-182] fused to [Gly-183 to Ala-219] ofSEQ ID NO:30; [Tyr-1 to Lys-47] fused to [Leu-48 to Thr-75] fused to[Ile-76 to Lys-94] fused to [Val-133 to Ala-182] of SEQ ID NO:30; or[Tyr-1 to Lys-47] fused to [Ile-76 to Lys-94] fused to [Val-133 toAla-182] fused to [Gly-183 to Ala-219] of SEQ ID NO:30. Othercombinations may include the polypeptide fragments in an order otherthan that recited above (e.g., [Tyr-1 to Lys-47] fused to [Gly-183 toAla-219] fused to [Val-133 to Ala-182] fused to [Leu-48 to Thr-75] ofSEQ ID NO:30). Other combinations may also include heterologouspolypeptide fragments as described herein and/or other polypeptides orpolypeptide fragments of the present invention (e.g., [Leu-48 to Thr-75]fused to [Ile-76 to Lys-94] fused to [Gly-95 to Gln-132] fused to[Val-133 to Ala-182] of SEQ ID NO:30 fused to an Fc receptor tag).Polynucleotides encoding any of these polypeptides are encompassed bythe invention.

Additional embodiments of the invention encompass Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide fragments comprising, oralternatively consisting of, functional regions of polypeptides of theinvention, such as the Garnier-Robson alpha-regions, beta-regions,turn-regions, and coil-regions, Chou-Fasman alpha-regions, beta-regions,and coil-regions, Kyte-Doolittle hydrophilic regions and hydrophobicregions, Eisenberg alpha- and beta-amphipathic regions, Karplus-Schulzflexible regions, Emini surface-forming regions and Jameson-Wolf regionsof high antigenic index set out in FIGS. 3 and 6 and in Table I and asdescribed herein. In a preferred embodiment, the polypeptide fragmentsof the invention are antigenic. The data presented in columns VIII, IX,XIII, and XIV of Table I can be used to routinely determine regions ofNeutrokine-alpha which exhibit a high degree of potential forantigenicity. Regions of high antigenicity are determined from the datapresented in columns VIII, IX, XIII, and/or IV by choosing values whichrepresent regions of the polypeptide which are likely to be exposed onthe surface of the polypeptide in an environment in which antigenrecognition may occur in the process of initiation of an immuneresponse. Among highly preferred fragments of the invention are thosethat comprise regions of Neutrokine-alpha and/or Neutrokine-alphaSV thatcombine several structural features, such as several (e.g., 1, 2, 3 or4) of the features set out above. Polynucleotides encoding thesepolypeptides are also encompassed by the invention.

In another embodiment, the invention provides a polypeptide comprising,or alternatively consisting of, an epitope-bearing portion of apolypeptide of the invention. Polynucleotides encoding thesepolypeptides are also encompassed by the invention. The epitope of thispolypeptide portion is an immunogenic or antigenic epitope of apolypeptide of the invention. An “immunogenic epitope” is defined as apart of a protein that elicits an antibody response when the wholeprotein is the immunogen. On the other hand, a region of a proteinmolecule to which an antibody can bind is defined as an “antigenicepitope.” The number of immunogenic epitopes of a protein generally isless than the number of antigenic epitopes. See, for instance, Geysen etal., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983).

As to the selection of polypeptides bearing an antigenic epitope (i.e.,that contain a region of a protein molecule to which an antibody canbind), it is well known in that art that relatively short syntheticpeptides that mimic part of a protein sequence are routinely capable ofeliciting an antiserum that reacts with the partially mimicked protein.See, for instance, Sutcliffe, J. G., Shinnick, T. M., Green, N. andLearner, R. A. (1983) “Antibodies that react with predetermined sites onproteins”, Science, 219:660-666. Peptides capable of elicitingprotein-reactive sera are frequently represented in the primary sequenceof a protein, can be characterized by a set of simple chemical rules,and are confined neither to immunodominant regions of intact proteins(i.e., immunogenic epitopes) nor to the amino or carboxyl terminals.Antigenic epitope-bearing peptides and polypeptides of the invention aretherefore useful to raise antibodies, including monoclonal antibodies,that bind specifically to a polypeptide of the invention. See, forinstance, Wilson et al., Cell 37:767-778 (1984) at 777.

Antigenic epitope-bearing peptides and polypeptides of the inventionpreferably contain a sequence of at least 4, at least 5, at least 6, atleast 7, more preferably at least 8, at least 9, at least 10, at least11, at least 12, at least 13, at least 14, at least 15, at least 20, atleast 25, at least 30, at least 40, at least 50, and, most preferably,between about 15 to about 30 amino acids contained within the amino acidsequence of a polypeptide of the invention. Preferred polypeptidescomprising immunogenic or antigenic epitopes are at least 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 aminoacid residues in length. Additional non-exclusive preferred antigenicepitopes include the antigenic epitopes disclosed herein, as well asportions thereof.

Non-limiting examples of antigenic polypeptides or peptides that can beused to generate Neutrokine-alpha- and/or Neutrokine-alphaSV-specificantibodies include: a polypeptide comprising, or alternativelyconsisting of, amino acid residues from about Phe-115 to about Leu-147in FIGS. 1A and 1B (SEQ ID NO:2); a polypeptide comprising, oralternatively consisting of, amino acid residues from about Ile-150 toabout Tyr-163 in FIGS. 1A and 1B (SEQ ID NO:2); a polypeptidecomprising, or alternatively consisting of, amino acid residues fromabout Ser-171 to about Phe-194 in FIGS. 1A and 1B (SEQ ID NO:2); apolypeptide comprising, or alternatively consisting of, amino acidresidues from about Glu-223 to about Tyr-246 in FIGS. 1A and 1B (SEQ IDNO:2); and a polypeptide comprising, or alternatively consisting of,amino acid residues from about Ser-271 to about Phe-278 in FIGS. 1A and1B (SEQ ID NO:2). In this context, “about” means the particularlyrecited ranges and ranges larger or smaller by several, a few, 5, 4, 3,2 or 1 amino acid residues at either or both the amino- andcarboxy-termini. These polypeptide fragments have been determined tobear antigenic epitopes of the Neutrokine-alpha polypeptide by theanalysis of the Jameson-Wolf antigenic index, as shown in FIG. 3 andTable I, above.

Non-limiting examples of antigenic polypeptides or peptides that can beused to generate Neutrokine-alpha- and/or Neutrokine-alphaSV-specificantibodies include: a polypeptide comprising, or alternativelyconsisting of, amino acid residues from about Pro-32 to about Leu-47 inFIGS. 5A and 5B (SEQ ID NO:19); a polypeptide comprising, oralternatively consisting of, amino acid residues from about Glu-116 toabout Ser-143 in FIGS. 5A and 5B (SEQ ID NO:19); a polypeptidecomprising, or alternatively consisting of, amino acid residues fromabout Phe-153 to about Tyr-173 in FIGS. 5A and 5B (SEQ ID NO:19); apolypeptide comprising, or alternatively consisting of, amino acidresidues from about Pro-218 to about Tyr-227 in FIGS. 5A and 5B (SEQ IDNO:19); a polypeptide comprising, or alternatively consisting of, aminoacid residues from about Ala-232 to about Gln-241 in FIGS. 5A and 5B(SEQ ID NO:19); a polypeptide comprising, or alternatively consistingof, amino acid residues from about Ile-244 to about Ala-249 in FIGS. 5Aand 5B (SEQ ID NO:19); and a polypeptide comprising, or alternativelyconsisting of, amino acid residues from about Ser-252 to about Val-257in FIGS. 5A and 5B (SEQ ID NO:19). In this context, “about” means theparticularly recited ranges and ranges larger or smaller by several, afew, 5, 4, 3, 2 or 1 amino acid residues at either or both the amino-and carboxy-termini. Polynucleotides encoding these polypeptides arealso encompassed by the invention. These polypeptide fragments have beendetermined to bear antigenic epitopes of the Neutrokine-alphaSVpolypeptide by the analysis of the Jameson-Wolf antigenic index, asshown in FIG. 6 and a tabular representation of the data presented inFIG. 6 generated by the Protean component of the DNA*STAR computerprogram (as set forth above).

The epitope-bearing peptides and polypeptides of the invention may beproduced by any conventional means. See, e.g., Houghten, R. A. (1985)General method for the rapid solid-phase synthesis of large numbers ofpeptides: specificity of antigen-antibody interaction at the level ofindividual amino acids. Proc. Natl. Acad. Sci. USA 82:5131-5135; this“Simultaneous Multiple Peptide Synthesis (SMPS)” process is furtherdescribed in U.S. Pat. No. 4,631,211 to Houghten et al. (1986).

Epitope-bearing peptides and polypeptides of the invention have usesthat include, but are not limited to, to induce antibodies according tomethods well known in the art. See, for instance, Sutcliffe et al.,supra; Wilson et al., supra; Chow, M. et al., Proc. Natl. Acad. Sci. USA82:910-914; and Bittle, F. J. et al., J. Gen. Virol. 66:2347-2354(1985). Immunogenic epitope-bearing peptides of the invention, i.e.,those parts of a protein that elicit an antibody response when the wholeprotein is the immunogen, are identified according to methods known inthe art. See, for instance, Geysen et al., supra. Further still, U.S.Pat. No. 5,194,392 to Geysen (1990) describes a general method ofdetecting or determining the sequence of monomers (amino acids or othercompounds) which is a topological equivalent of the epitope (i.e., a“mimotope”) which is complementary to a particular paratope (antigenbinding site) of an antibody of interest. More generally, U.S. Pat. No.4,433,092 to Geysen (1989) describes a method of detecting ordetermining a sequence of monomers which is a topographical equivalentof a ligand which is complementary to the ligand binding site of aparticular receptor of interest. Similarly, U.S. Pat. No. 5,480,971 toHoughten, R. A. et al. (1996) on Peralkylated Oligopeptide Mixturesdiscloses linear C1-C7-alkyl peralkylated oligopeptides and sets andlibraries of such peptides, as well as methods for using sucholigopeptide sets and libraries for determining the sequence of aperalkylated oligopeptide that preferentially binds to an acceptormolecule of interest. Thus, non-peptide analogs of the epitope-bearingpeptides of the invention also can be made routinely by these methods.

The present invention encompasses polypeptides comprising, oralternatively consisting of, an epitope of the polypeptide having anamino acid sequence of SEQ ID NO:2, or an epitope of the polypeptidesequence encoded by a polynucleotide sequence contained in ATCC depositNo. 97768, or encoded by a polynucleotide that hybridizes to thecomplement of the sequence of SEQ ID NO:1 or the cDNA sequence containedin ATCC deposit No. 97768 (e.g., under hybridization conditionsdescribed herein). The present invention further encompassespolynucleotide sequences comprising, or alternatively consisting of, asequence encoding an epitope of a polypeptide sequence of the invention(such as, for example, the sequence disclosed in SEQ ID NO:1),polynucleotide sequences of the complementary strand of a polynucleotidesequence encoding an epitope of the invention, and polynucleotidesequences which hybridize to the complementary strand (e.g., underhybridization conditions described herein).

The present invention also encompasses polypeptides comprising, oralternatively consisting of, an epitope of the polypeptide having anamino acid sequence of SEQ ID NO:19, or an epitope of the polypeptidesequence encoded by a polynucleotide sequence contained in ATCC depositNo. 203518, or encoded by a polynucleotide that hybridizes to thecomplement of the sequence of SEQ ID NO:18 or the cDNA sequencecontained in ATCC deposit No. 203518 (e.g., under hybridizationconditions described herein). The present invention further encompassespolynucleotide sequences comprising, or alternatively consisting of, asequence encoding an epitope of a polypeptide sequence of the invention(such as, for example, the sequence disclosed in SEQ ID NO:18),polynucleotide sequences of the complementary strand of a polynucleotidesequence encoding an epitope of the invention, and polynucleotidesequences which hybridize to the complementary strand (e.g., underhybridization conditions described herein).

The term “epitopes,” as used herein, refers to portions of a polypeptidehaving antigenic or immunogenic activity in an animal, preferably amammal, and most preferably in a human. In a preferred embodiment, thepresent invention encompasses a polypeptide comprising an epitope, aswell as the polynucleotide encoding this polypeptide. An “immunogenicepitope,” as used herein, is defined as a portion of a protein thatelicits an antibody response in an animal, as determined by any methodknown in the art, for example, by the methods for generating antibodiesdescribed infra. (See, for example, Geysen et al., Proc. Natl. Acad.Sci. USA 81:3998-4002 (1983)). The term “antigenic epitope,” as usedherein, is defined as a portion of a protein to which an antibody canimmunospecifically bind its antigen as determined by any method wellknown in the art, for example, by the immunoassays described herein.Immunospecific binding excludes non-specific binding but does notnecessarily exclude cross-reactivity with other antigens. Antigenicepitopes need not necessarily be immunogenic.

Fragments which function as epitopes may be produced by any conventionalmeans. (See, e.g., Houghten, Proc. Natl. Acad. Sci. USA 82:5131-5135(1985), further described in U.S. Pat. No. 4,631,211).

In the present invention, antigenic epitopes preferably contain asequence of at least 4, at least 5, at least 6, at least 7, morepreferably at least 8, at least 9, at least 10, at least 11, at least12, at least 13, at least 14, at least 15, at least 20, at least 25, atleast 30, at least 40, at least 50, and, most preferably, between about15 to about 30 amino acids. Preferred polypeptides comprisingimmunogenic or antigenic epitopes are at least 10, 15, 20, 25, 30, 35,40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 amino acidresidues in length. Additional non-exclusive preferred antigenicepitopes include the antigenic epitopes disclosed herein, as well asportions thereof. Antigenic epitopes are useful, for example, to raiseantibodies, including monoclonal antibodies, that specifically bind theepitope. Preferred antigenic epitopes include the antigenic epitopesdisclosed herein, as well as any combination of two, three, four, fiveor more of these antigenic epitopes. Antigenic epitopes can be used asthe target molecules in immunoassays. (See, for instance, Wilson et al.,Cell 37:767-778 (1984); Sutcliffe et al., Science 219:660-666 (1983)).

Similarly, immunogenic epitopes can be used, for example, to induceantibodies according to methods well known in the art. (See, forinstance, Sutcliffe et al., supra; Wilson et al., supra; Chow et al.,Proc. Natl. Acad. Sci. USA 82:910-914; and Bittle et al., J. Gen. Virol.66:2347-2354 (1985). Preferred immunogenic epitopes include theimmunogenic epitopes disclosed herein, as well as any combination oftwo, three, four, five or more of these immunogenic epitopes. Thepolypeptides comprising one or more immunogenic epitopes may bepresented for eliciting an antibody response together with a carrierprotein, such as an albumin, to an animal system (such as rabbit ormouse), or, if the polypeptide is of sufficient length (at least about25 amino acids), the polypeptide may be presented without a carrier.However, immunogenic epitopes comprising as few as 8 to 10 amino acidshave been shown to be sufficient to raise antibodies capable of bindingto, at the very least, linear epitopes in a denatured polypeptide (e.g.,in Western blotting).

Epitope-bearing polypeptides of the present invention may be used toinduce antibodies according to methods well known in the art including,but not limited to, in vivo immunization, in vitro immunization, andphage display methods. See, e.g., Sutcliffe et al., supra; Wilson etal., supra, and Bittle et al., J. Gen. Virol., 66:2347-2354 (1985). Ifin vivo immunization is used, animals may be immunized with freepeptide; however, anti-peptide antibody titer may be boosted by couplingthe peptide to a macromolecular carrier, such as keyhole limpethemacyanin (KLH) or tetanus toxoid. For instance, peptides containingcysteine residues may be coupled to a carrier using a linker such asmaleimidobenzoyl-N-hydroxysuccinimide ester (MBS), while other peptidesmay be coupled to carriers using a more general linking agent such asglutaraldehyde. Animals such as rabbits, rats and mice are immunizedwith either free or carrier-coupled peptides, for instance, byintraperitoneal and/or intradermal injection of emulsions containingabout 100 micrograms of peptide or carrier protein and Freund's adjuvantor any other adjuvant known for stimulating an immune response. Severalbooster injections may be needed, for instance, at intervals of abouttwo weeks, to provide a useful titer of anti-peptide antibody which canbe detected, for example, by ELISA assay using free peptide adsorbed toa solid surface. The titer of anti-peptide antibodies in serum from animmunized animal may be increased by selection of anti-peptideantibodies, for instance, by adsorption to the peptide on a solidsupport and elution of the selected antibodies according to methods wellknown in the art.

As one of skill in the art will appreciate, and as discussed above, thepolypeptides of the present invention comprising an immunogenic orantigenic epitope can be fused to other polypeptide sequences. Forexample, the polypeptides of the present invention may be fused with theconstant domain of immunoglobulins (IgA, IgE, IgG, IgM), or portionsthereof (CH1, CH2, CH3, or any combination thereof and portions thereof)resulting in chimeric polypeptides. Such fusion proteins may facilitatepurification and may increase half-life in vivo. This has been shown forchimeric proteins consisting of the first two domains of the humanCD4-polypeptide and various domains of the constant regions of the heavyor light chains of mammalian immunoglobulins. See, e.g., EP 394,827;Traunecker et al., Nature, 331:84-86 (1988). Enhanced delivery of anantigen across the epithelial barrier to the immune system has beendemonstrated for antigens (e.g., insulin) conjugated to an FcRn bindingpartner such as IgG or Fc fragments (see, e.g., PCT Publications WO96/22024 and WO 99/04813). IgG Fusion proteins that have adisulfide-linked dimeric structure due to the IgG portion disulfidebonds have also been found to be more efficient in binding andneutralizing other molecules than monomeric polypeptides or fragmentsthereof alone. See, e.g., Fountoulakis et al., J. Biochem.,270:3958-3964 (1995). Nucleic acids encoding the above epitopes can alsobe recombined with a gene of interest as an epitope tag (e.g., thehemagglutinin (“HA”) tag or flag tag) to aid in detection andpurification of the expressed polypeptide. For example, a systemdescribed by Janknecht et al. allows for the ready purification ofnon-denatured fusion proteins expressed in human cell lines (Janknechtet al., 1991, Proc. Natl. Acad. Sci. USA 88:8972-897). In this system,the gene of interest is subcloned into a vaccinia recombination plasmidsuch that the open reading frame of the gene is translationally fused toan amino-terminal tag consisting of six histidine residues. The tagserves as a matrix-binding domain for the fusion protein. Extracts fromcells infected with the recombinant vaccinia virus are loaded onto Ni²⁺nitriloacetic acid-agarose column and histidine-tagged proteins can beselectively eluted with imidazole-containing buffers.

In another embodiment, the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the present invention and the epitope-bearing fragmentsthereof are fused with a heterologous antigen (e.g., polypeptide,carbohydrate, phospholipid, or nucleic acid). In specific embodiments,the heterologous antigen is an immunogen.

In a more specific embodiment, the heterologous antigen is the gp120protein of HIV, or a fragment thereof. Polynucleotides encoding thesepolypeptides are also encompassed by the invention.

In another embodiment, the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the present invention and the epitope-bearing fragmentsthereof are fused with polypeptide sequences of another TNF ligandfamily member (or biologically active fragments or variants thereof). Ina specific embodiment, the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the present invention are fused with a CD40L polypeptidesequence. In a preferred embodiment, the CD40L polypeptide sequence issoluble.

The techniques of gene-shuffling, motif-shuffling, exon-shuffling,and/or codon-shuffling (collectively referred to as “DNA shuffling”) maybe employed to modulate the activities of Neutrokine-alpha and/orNeutrokine-alphaSV thereby effectively generating agonists andantagonists of Neutrokine-alpha and/or Neutrokine-alphaSV. Seegenerally, U.S. Pat. Nos. 5,605,793, 5,811,238, 5,830,721, 5,834,252,and 5,837,458, and Patten, P. A., et al., Curr. Opinion Biotechnol.8:724-33 (1997); Harayama, S. Trends Biotechnol. 16(2):76-82 (1998);Hansson, L. O., et al., J. Mol. Biol. 287:265-76 (1999); and Lorenzo, M.M. and Blasco, R. Biotechniques 24(2):308-13 (1998) (each of thesepatents and publications are hereby incorporated by reference). In oneembodiment, alteration of Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides and corresponding polypeptides may be achieved by DNAshuffling. DNA shuffling involves the assembly of two or more DNAsegments into a desired Neutrokine-alpha and/or Neutrokine-alphaSVmolecule by homologous, or site-specific, recombination. In anotherembodiment, Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotidesand corresponding polypeptides may be altered by being subjected torandom mutagenesis by error-prone PCR, random nucleotide insertion orother methods prior to recombination. In another embodiment, one or morecomponents, motifs, sections, parts, domains, fragments, etc., ofNeutrokine-alpha and/or Neutrokine-alphaSV may be recombined with one ormore components, motifs, sections, parts, domains, fragments, etc. ofone or more heterologous molecules. In preferred embodiments, theheterologous molecules are, for example, TNF-alpha, lymphotoxin-alpha(LT-alpha, also known as TNF-beta), LT-beta (found in complexheterotrimer LT-alpha2-beta), OPGL, FasL, CD27L, CD30L, CD40L, 4-1BBL,DcR3, OX40L, TNF-gamma (International Publication No. WO 96/14328),AIM-I (International Publication No. WO 97/33899), AIM-II (InternationalPublication No. WO 97/34911), APRIL (J. Exp. Med. 188(6):1185-1190),endokine-alpha (International Publication No. WO 98/07880), OPG, OX40,and nerve growth factor (NGF), and soluble forms of Fas, CD30, CD27,CD40 and 4-IBB, TR2 (International Publication No. WO 96/34095), DR3(International Publication No. WO 97/33904), DR4 (InternationalPublication No. WO 98/32856), TR5 (International Publication No. WO98/30693), TR6 (International Publication No. WO 98/30694), TR7(International Publication No. WO 98/41629), TRANK, TR9 (InternationalPublication No. WO 98/56892), TR10 (International Publication No. WO98/54202), 312C2 (International Publication No. WO 98/06842), TR12, CAD,and v-FLIP. In further embodiments, the heterologous molecules are anymember of the TNF family.

In a preferred embodiments, Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the invention (including biologically active fragmentsor variants thereof), are fused with soluble CD40L polypeptides, orbiologically active fragments or variants thereof.

To improve or alter the characteristics of Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides, protein engineering may be employed.Recombinant DNA technology known to those skilled in the art can be usedto create novel mutant proteins or “muteins including single or multipleamino acid substitutions, deletions, additions or fusion proteins. Suchmodified polypeptides can show, e.g., enhanced activity or increasedstability. In addition, they may be purified in higher yields and showbetter solubility than the corresponding natural polypeptide, at leastunder certain purification and storage conditions. For instance, formany proteins, including the extracellular domain or the mature form(s)of a secreted protein, it is known in the art that one or more aminoacids may be deleted from the N-terminus or C-terminus withoutsubstantial loss of biological function. For instance, Ron et al., J.Biol. Chem., 268:2984-2988 (1993) reported modified KGF proteins thathad heparin binding activity even if 3, 8, or 27 amino-terminal aminoacid residues were missing.

In the present case, since the protein of the invention is a member ofthe TNF polypeptide family, deletions of N-terminal amino acids up tothe Gly (G) residue at position 191 in FIGS. 1A and 1B (SEQ ID NO:2) mayretain some biological activity such as, for example, the ability tostimulate lymphocyte (e.g., B cell) proliferation, differentiation,and/or activation, and cytotoxicity to appropriate target cells.Polypeptides having further N-terminal deletions including the Gly (G)residue would not be expected to retain biological activities because itis known that this residue in TNF-related polypeptides is in thebeginning of the conserved domain required for biological activities.However, even if deletion of one or more amino acids from the N-terminusof a protein results in modification or loss of one or more biologicalfunctions of the protein, other functional activities may still beretained. Thus, the ability of the shortened protein to induce and/orbind to antibodies which recognize the complete or extracellular domainof the protein generally will be retained when less than the majority ofthe residues of the complete or extracellular domain of the protein areremoved from the N-terminus. Whether a particular polypeptide lackingN-terminal residues of a complete protein retains such immunologicactivities can readily be determined by routine methods described hereinand otherwise known in the art.

Accordingly, the present invention further provides polypeptides havingone or more residues deleted from the amino terminus of the amino acidsequence of the Neutrokine-alpha shown in FIGS. 1A and 1B (SEQ ID NO:2),up to the glycine residue at position 191 (Gly-191 residue from theamino terminus), and polynucleotides encoding such polypeptides. Inparticular, the present invention provides polypeptides comprising, oralternatively consisting of, the amino acid sequence of residues n¹-285of SEQ ID NO:2, where n¹ is an integer in the range of the amino acidposition of amino acid residues 2-190 of the amino acid sequence in SEQID NO:2. Polynucleotides encoding these polypeptides are alsoencompassed by the invention. More in particular, the invention providespolynucleotides encoding polypeptides comprising, or alternativelyconsisting of, an amino acid sequence selected from the group consistingof residues 2-285, 3-285, 4-285, 5-285, 6-285, 7-285, 8-285, 9-285,10-285, 11-285, 12-285, 13-285, 14-285, 15-285, 16-285, 17-285, 18-285,19-285, 20-285, 21-285, 22-285, 23-285, 24-285, 25-285, 26-285, 27-285,28-285, 29-285, 30-285, 31-285, 32-285, 33-285, 34-285, 35-285, 36-285,37-285, 38-285, 39-285, 40-285, 41-285, 42-285, 43-285, 44-285, 45-285,46-285, 47-285, 48-285, 49-285, 50-285, 51-285, 52-285, 53-285, 54-285,55-285, 56-285, 57-285, 58-285, 59-285, 60-285, 61-285, 62-285, 63-285,64-285, 65-285, 66-285, 67-285, 68-285, 69-285, 70-285, 71-285, 72-285,73-285, 74-285, 75-285, 76-285, 77-285, 78-285, 79-285, 80-285, 81-285,82-285, 83-285, 84-285, 85-285, 86-285, 87-285, 88-285, 89-285, 90-285,91-285, 92-285, 93-285, 94-285, 95-285, 96-285, 97-285, 98-285, 99-285,100-285, 101-285, 102-285, 103-285, 104-285, 105-285, 106-285, 107-285,108-285, 109-285, 110-285, 111-285, 112-285, 113-285, 114-285, 115-285,116-285, 117-285, 118-285, 119-285, 120-285, 121-285, 122-285, 123-285,124-285, 125-285, 126-285, 127-285, 128-285, 129-285, 130-285, 131-285,132-285, 133-285, 134-285, 135-285, 136-285, 137-285, 138-285, 139-285,140-285, 141-285, 142-285, 143-285, 144-285, 145-285, 146-285, 147-285,148-285, 149-285, 150-285, 151-285, 152-285, 153-285, 154-285, 155-285,156-285, 157-285, 158-285, 159-285, 160-285, 161-285, 162-285, 163-285,164-285, 165-285, 166-285, 167-285, 168-285, 169-285, 170-285, 171-285,172-285, 173-285, 174-285, 175-285, 176-285, 177-285, 178-285, 179-285,180-285, 181-285, 182-285, 183-285, 184-285, 185-285, 186-285, 187-285,188-285, 189-285, and 190-285 of SEQ ID NO:2. Polypeptides encoded bythese polynucleotides are also encompassed by the invention. The presentinvention is also directed to nucleic acid molecules comprising, oralternatively, consisting of, a polynucleotide sequence at least 80%,85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to the polynucleotidesequence encoding the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides described above. The present invention also encompasses theabove polynucleotide sequences fused to a heterologous polynucleotidesequence. Polypeptides encoded by these nucleic acids and/orpolynucleotide sequences are also encompassed by the invention, as arepolypeptides comprising, or alternatively consisting of, an amino acidsequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99%identical to the amino acid sequence described above, andpolynucleotides that encode such polypeptides.

Furthermore, since the predicted extracellular domain of theNeutrokine-alpha polypeptides of the invention may itself elicitbiological activity, deletions of N- and C-terminal amino acid residuesfrom the predicted extracellular region of the polypeptide (spanningpositions Gln-73 to Leu-285 of SEQ ID NO:2) may retain some biologicalactivity such as, for example, ligand binding, stimulation of lymphocyte(e.g., B cell) proliferation, differentiation, and/or activation, andmodulation of cell replication or modulation of target cell activities.However, even if deletion of one or more amino acids from the N-terminusof the predicted extracellular domain of a Neutrokine-alpha polypeptideresults in modification or loss of one or more biological functions ofthe polypeptide, other functional activities may still be retained.Thus, the ability of the shortened polypeptides to induce and/or bind toantibodies which recognize the complete or mature or extracellulardomains of the polypeptides generally will be retained when less thanthe majority of the residues of the complete or mature or extracellulardomains of the polypeptides are removed from the N-terminus. Whether aparticular polypeptide lacking N-terminal residues of a completepolypeptide retains such immunologic activities can readily bedetermined by routine methods described herein and otherwise known inthe art.

Accordingly, the present invention further provides polypeptides havingone or more residues deleted from the amino terminus of the amino acidsequence of Neutrokine-alpha shown in SEQ ID NO:2, up to the glycineresidue at position number 280, and polynucleotides encoding suchpolypeptides. In particular, the present invention provides polypeptidescomprising, or alternatively consisting of, the amino acid sequence ofresidues n²-285 of SEQ ID NO:2, where n² is an integer in the range ofthe amino acid position of amino acid residues 73-280 in SEQ ID NO:2,and 73 is the position of the first residue from the N-terminus of thepredicted extracellular domain of the Neutrokine-alpha polypeptide(disclosed in SEQ ID NO:2). Polynucleotides encoding these polypeptidesare also encompassed by the invention. More in particular, in certainembodiments, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, an amino acidsequence selected from the group consisting of residues of Q-73 toL-285; G-74 to L-285; D-75 to L-285; L-76 to L-285; A-77 to L-285; S-78to L-285; L-79 to L-285; R-80 to L-285; A-81 to L-285; E-82 to L-285;L-83 to L-285; Q-84 to L-285; G-85 to L-285; H-86 to L-285; H-87 toL-285; A-88 to L-285; E-89 to L-285; K-90 to L-285; L-91 to L-285; P-92to L-285; A-93 to L-285; G-94 to L-285; A-95 to L-285; G-96 to L-285;A-97 to L-285; P-98 to L-285; K-99 to L-285; A-100 to L-285; G-101 toL-285; L-102 to L-285; E-103 to L-285; E-104 to L-285; A-105 to L-285;P-106 to L-285; A-107 to L-285; V-108 to L-285; T-109 to L-285; A-110 toL-285; G-111 to L-285; L-112 to L-285; K-113 to L-285; I-114 to L-285;F-115 to L-285; E-116 to L-285; P-117 to L-285; P-118 to L-285; A-119 toL-285; P-120 to L-285; G-121 to L-285; E-122 to L-285; G-123 to L-285;N-124 to L-285; S-125 to L-285; S-126 to L-285; Q-127 to L-285; N-128 toL-285; S-129 to L-285; R-130 to L-285; N-131 to L-285; K-132 to L-285;R-133 to L-285; A-134 to L-285; V-135 to L-285; Q-136 to L-285; G-137 toL-285; P-138 to L-285; E-139 to L-285; E-140 to L-285; T-141 to L-285;V-142 to L-285; T-143 to L-285; Q-144 to L-285; D-145 to L-285; C-146 toL-285; L-147 to L-285; Q-148 to L-285; L-149 to L-285; I-150 to L-285;A-151 to L-285; D-152 to L-285; S-153 to L-285; E-154 to L-285; T-155 toL-285; P-156 to L-285; T-157 to L-285; I-158 to L-285; Q-159 to L-285;K-160 to L-285; G-161 to L-285; S-162 to L-285; Y-163 to L-285; T-164 toL-285; F-165 to L-285; V-166 to L-285; P-167 to L-285; W-168 to L-285;L-169 to L-285; L-170 to L-285; S-171 to L-285; F-172 to L-285; K-173 toL-285; R-174 to L-285; G-175 to L-285; S-176 to L-285; A-177 to L-285;L-178 to L-285; E-179 to L-285; E-180 to L-285; K-181 to L-285; E-182 toL-285; N-183 to L-285; K-184 to L-285; I-185 to L-285; L-186 to L-285;V-187 to L-285; K-188 to L-285; E-189 to L-285; T-190 to L-285; G-191 toL-285; Y-192 to L-285; F-193 to L-285; F-194 to L-285; I-195 to L-285;Y-196 to L-285; G-197 to L-285; Q-198 to L-285; V-199 to L-285; L-200 toL-285; Y-201 to L-285; T-202 to L-285; D-203 to L-285; K-204 to L-285;T-205 to L-285; Y-206 to L-285; A-207 to L-285; M-208 to L-285; G-209 toL-285; H-210 to L-285; L-211 to L-285; I-212 to L-285; Q-213 to L-285;R-214 to L-285; K-215 to L-285; K-216 to L-285; V-217 to L-285; H-218 toL-285; V-219 to L-285; F-220 to L-285; G-221 to L-285; D-222 to L-285;E-223 to L-285; L-224 to L-285; S-225 to L-285; L-226 to L-285; V-227 toL-285; T-228 to L-285; L-229 to L-285; F-230 to L-285; R-231 to L-285;C-232 to L-285; I-233 to L-285; Q-234 to L-285; N-235 to L-285; M-236 toL-285; P-237 to L-285; E-238 to L-285; T-239 to L-285; L-240 to L-285;P-241 to L-285; N-242 to L-285; N-243 to L-285; S-244 to L-285; C-245 toL-285; Y-246 to L-285; S-247 to L-285; A-248 to L-285; G-249 to L-285;I-250 to L-285; A-251 to L-285; K-252 to L-285; L-253 to L-285; E-254 toL-285; E-255 to L-285; G-256 to L-285; D-257 to L-285; E-258 to L-285;L-259 to L-285; Q-260 to L-285; L-261 to L-285; A-262 to L-285; I-263 toL-285; P-264 to L-285; R-265 to L-285; E-266 to L-285; N-267 to L-285;A-268 to L-285; Q-269 to L-285; I-270 to L-285; S-271 to L-285; L-272 toL-285; D-273 to L-285; G-274 to L-285; D-275 to L-285; V-276 to L-285;T-277 to L-285; F-278 to L-285; F-279 to L-285; and G-280 to L-285 ofSEQ ID NO:2. Polypeptides encoded by these polynucleotides are alsoencompassed by the invention. The present invention is also directed tonucleic acid molecules comprising, or alternatively, consisting of, apolynucleotide sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%or 99% identical to the polynucleotide sequence encoding theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides described above.The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these nucleic acids and/or polynucleotide sequences are alsoencompassed by the invention, as are polypeptides comprising, oralternatively consisting of, an amino acid sequence at least 80%, 85%,90%, 92%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequencedescribed above, and polynucleotides that encode such polypeptides.

Highly preferred embodiments of the invention are directed to nucleicacid molecules comprising, or alternatively consisting of apolynucleotide having a nucleotide sequence at least 80%, 85%, 90%identical and more preferably at least 95%, 96%, 97%, 98%, 99% or 100%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). Preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 90%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). More preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 95%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2). More preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 96%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2).

Additionally, more preferred embodiments of the invention are directedto nucleic acid molecules comprising, or alternatively consisting of apolynucleotide having a nucleotide sequence at least 97% to apolynucleotide sequence encoding the Neutrokine-alpha polypeptide havingthe amino acid sequence at positions 134-285 in FIGS. 1A and 1B (SEQ IDNO:2). Additionally, more preferred embodiments of the invention aredirected to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 98%to a polynucleotide sequence encoding the Neutrokine-alpha polypeptidehaving the amino acid sequence at positions 134-285 in FIGS. 1A and 1B(SEQ ID NO:2). Additionally, more preferred embodiments of the inventionare directed to nucleic acid molecules comprising, or alternativelyconsisting of a polynucleotide having a nucleotide sequence at least 99%identical to a polynucleotide sequence encoding the Neutrokine-alphapolypeptide having the amino acid sequence at positions 134-285 in FIGS.1A and 1B (SEQ ID NO:2).

In specific embodiments, a polypeptide comprising, or alternativelyconsisting of, one of the following N-terminally deleted polypeptidefragments of Neutrokine-alpha and/or Neutrokine-alphaSV are preferred:amino acid residues Ala-71 through Leu-285, amino acid residues Ala-81through Leu-285, amino acid residues Leu-112 through Leu-285, amino acidresidues Ala-134 through Leu-285, amino acid residues Leu-147 throughLeu-285, and amino acid residues Gly-161 through Leu-285 of SEQ ID NO:2.Polynucleotides encoding these polypeptides are also encompassed by theinvention.

Similarly, many examples of biologically functional C-terminal deletionmuteins are known. For instance, Interferon gamma shows up to ten timeshigher activities by deleting 8-10 amino acid residues from the carboxyterminus of the protein (Döbeli et al., J. Biotechnology 7:199-216(1988). Since the present protein is a member of the TNF polypeptidefamily, deletions of C-terminal amino acids up to the leucine residue atposition 284 are expected to retain most if not all biological activitysuch as, for example, ligand binding, the ability to stimulatelymphocyte (e.g., B cell) proliferation, differentiation, and/oractivation, and modulation of cell replication. Polypeptides havingdeletions of up to about 10 additional C-terminal residues (i.e., up tothe glycine residue at position 274) also may retain some activity suchas receptor binding, although such polypeptides would lack a portion ofthe conserved TNF domain which extends to about Leu-284 of SEQ ID NO:2.However, even if deletion of one or more amino acids from the C-terminusof a protein results in modification or loss of one or more biologicalfunctions of the protein, other functional activities may still beretained. Thus, the ability of the shortened protein to induce and/orbind to antibodies which recognize the complete or mature proteingenerally will be retained when less than the majority of the residuesof the complete or mature protein are removed from the C-terminus.Whether a particular polypeptide lacking C-terminal residues of acomplete protein retains such immunologic activities can readily bedetermined by routine methods described herein and otherwise known inthe art.

Accordingly, the present invention further provides polypeptides havingone or more residues deleted from the carboxy terminus of the amino acidsequence of the Neutrokine-alpha polypeptide shown in FIGS. 1A and 1B(SEQ ID NO:2), up to the glycine residue at position 274 (Gly-274) andpolynucleotides encoding such polypeptides. In particular, the presentinvention provides polypeptides comprising, or alternatively consistingof, the amino acid sequence of residues 1-m¹ of the amino acid sequencein SEQ ID NO:2, where m¹ is any integer in the range of the amino acidposition of amino acid residues 274-284 in SEQ ID NO:2. Polynucleotidesencoding these polypeptides are also encompassed by the invention. Morein particular, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, an amino acidsequence selected from the group consisting of residues 1-274, 1-275,1-276, 1-277, 1-278, 1-279, 1-280, 1-281, 1-282, 1-283 and 1-284 of SEQID NO:2. Polypeptides encoded by these polynucleotides are alsoencompassed by the invention. The present invention is also directed tonucleic acid molecules comprising, or alternatively, consisting of, apolynucleotide sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%or 99% identical to the polynucleotide sequence encoding theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides described above.The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these nucleic acids and/or polynucleotide sequences are alsoencompassed by the invention, as are polypeptides comprising, oralternatively consisting of, an amino acid sequence at least 80%, 85%,90%, 92%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequencedescribed above, and polynucleotides that encode such polypeptides.

Also provided are polypeptides comprising, or alternatively consistingof, one or more amino acids deleted from both the amino and the carboxyltermini, which may be described generally as having residues n¹-m¹ ofSEQ ID NO:2, where n¹ and m¹ are integers as defined above. Alsoincluded are a nucleotide sequence encoding a polypeptide comprising, oralternatively consisting of, a portion of the complete Neutrokine-alphaamino acid sequence encoded by the deposited cDNA clone contained inATCC Accession No. 97768 where this portion excludes from 1 to 190 aminoacids from the amino terminus or from 1 to 11 amino acids from theC-terminus of the complete amino acid sequence (or any combination ofthese N-terminal and C-terminal deletions) encoded by the cDNA clone inthe deposited plasmid. Polynucleotides encoding all of the abovedeletion polypeptides are encompassed by the invention.

Similarly, deletions of C-terminal amino acid residues of the predictedextracellular domain of Neutrokine-alpha up to the leucine residue atposition 79 of SEQ ID NO:2 may retain some biological activity, such as,for example, ligand binding, stimulation of lymphocyte (e.g., B cell)proliferation, differentiation, and/or activation, and modulation ofcell replication or modulation of target cell activities. Polypeptideshaving further C-terminal deletions including Leu-79 of SEQ ID NO:2would not be expected to retain biological activities.

However, even if deletion of one or more amino acids from the C-terminusof a polypeptide results in modification or loss of one or morebiological functions of the polypeptide, other functional activities maystill be retained. Thus, the ability of the shortened polypeptide toinduce and/or bind to antibodies which recognize the complete, mature orextracellular forms of the polypeptide generally will be retained whenless than the majority of the residues of the complete, mature orextracellular forms of the polypeptide are removed from the C-terminus.Whether a particular polypeptide lacking C-terminal residues of thepredicted extracellular domain retains such immunologic activities canreadily be determined by routine methods described herein and otherwiseknown in the art.

Accordingly, the present invention further provides polypeptides havingone or more residues deleted from the carboxy terminus of the amino acidsequence of the predicted extracellular domain of Neutrokine-alphapolypeptide shown in SEQ ID NO:2, up to the leucine residue at position79 of SEQ ID NO:2, and polynucleotides encoding such polypeptides. Inparticular, the present invention provides polypeptides comprising, oralternatively consisting of, the amino acid sequence of residues 73-m²of the amino acid sequence in SEQ ID NO:2, where m² is any integer inthe range of the amino acid position of amino acid residues 79 to 285 inthe amino acid sequence in SEQ ID NO:2, and residue 78 is the positionof the first residue at the C-terminus of the predicted extracellulardomain of the Neutrokine-alpha polypeptide (disclosed in SEQ ID NO:2).Polypeptides encoded by these polynucleotides are also encompassed bythe invention. More in particular, in certain embodiments, the inventionprovides polynucleotides encoding polypeptides comprising, oralternatively consisting of, an amino acid sequence selected from thegroup consisting of residues Q-73 to Leu-285; Q-73 to L-284; Q-73 toK-283; Q-73 to L-282; Q-73 to A-281; Q-73 to G-280; Q-73 to F-279; Q-73to F-278; Q-73 to T-277; Q-73 to V-276; Q-73 to D-275; Q-73 to G-274;Q-73 to D-273; Q-73 to L-272; Q-73 to S-271; Q-73 to I-270; Q-73 toQ-269; Q-73 to A-268; Q-73 to N-267; Q-73 to E-266; Q-73 to R-265; Q-73to P-264; Q-73 to I-263; Q-73 to A-262; Q-73 to L-261; Q-73 to Q-260;Q-73 to L-259; Q-73 to E-258; Q-73 to D-257; Q-73 to G-256; Q-73 toE-255; Q-73 to E-254; Q-73 to L-253; Q-73 to K-252; Q-73 to A-251; Q-73to I-250; Q-73 to G-249; Q-73 to A-248; Q-73 to S-247; Q-73 to Y-246;Q-73 to C-245; Q-73 to S-244; Q-73 to N-243; Q-73 to N-242; Q-73 toP-241; Q-73 to L-240; Q-73 to T-239; Q-73 to E-238; Q-73 to P-237; Q-73to M-236; Q-73 to N-235; Q-73 to Q-234; Q-73 to I-233; Q-73 to C-232;Q-73 to R-231; Q-73 to F-230; Q-73 to L-229; Q-73 to T-228; Q-73 toV-227; Q-73 to L-226; Q-73 to S-225; Q-73 to L-224; Q-73 to E-223; Q-73to D-222; Q-73 to G-221; Q-73 to F-220; Q-73 to V-219; Q-73 to H-218;Q-73 to V-217; Q-73 to K-216; Q-73 to K-215; Q-73 to R-214; Q-73 toQ-213; Q-73 to I-212; Q-73 to L-211; Q-73 to H-210; Q-73 to G-209; Q-73to M-208; Q-73 to A-207; Q-73 to Y-206; Q-73 to T-205; Q-73 to K-204;Q-73 to D-203; Q-73 to T-202; Q-73 to Y-201; Q-73 to L-200; Q-73 toV-199; Q-73 to Q-198; Q-73 to G-197; Q-73 to Y-196; Q-73 to I-195; Q-73to F-194; Q-73 to F-193; Q-73 to Y-192; Q-73 to G-191; Q-73 to T-190;Q-73 to E-189; Q-73 to K-188; Q-73 to V-187; Q-73 to L-186; Q-73 toI-185; Q-73 to K-184; Q-73 to N-183; Q-73 to E-182; Q-73 to K-181; Q-73to E-180; Q-73 to E-179; Q-73 to L-178; Q-73 to A-177; Q-73 to S-176;Q-73 to G-175; Q-73 to R-174; Q-73 to K-173; Q-73 to F-172; Q-73 toS-171; Q-73 to L-170; Q-73 to L-169; Q-73 to W-168; Q-73 to P-167; Q-73to V-166; Q-73 to F-165; Q-73 to T-164; Q-73 to Y-163; Q-73 to S-162;Q-73 to G-161; Q-73 to K-160; Q-73 to Q-159; Q-73 to I-158; Q-73 toT-157; Q-73 to P-156; Q-73 to T-155; Q-73 to E-154; Q-73 to S-153; Q-73to D-152; Q-73 to A-151; Q-73 to I-150; Q-73 to L-149; Q-73 to Q-148;Q-73 to L-147; Q-73 to C-146; Q-73 to D-145; Q-73 to Q-144; Q-73 toT-143; Q-73 to V-142; Q-73 to T-141; Q-73 to E-140; Q-73 to E-139; Q-73to P-138; Q-73 to G-137; Q-73 to Q-136; Q-73 to V-135; Q-73 to A-134;Q-73 to R-133; Q-73 to K-132; Q-73 to N-131; Q-73 to R-130; Q-73 toS-129; Q-73 to N-128; Q-73 to Q-127; Q-73 to S-126; Q-73 to S-125; Q-73to N-124; Q-73 to G-123; Q-73 to E-122; Q-73 to G-121; Q-73 to P-120;Q-73 to A-119; Q-73 to P-118; Q-73 to P-117; Q-73 to E-116; Q-73 toF-115; Q-73 to I-114; Q-73 to K-113; Q-73 to L-112; Q-73 to G-111; Q-73to A-110; Q-73 to T-109; Q-73 to V-108; Q-73 to A-107; Q-73 to P-106;Q-73 to A-105; Q-73 to E-104; Q-73 to E-103; Q-73 to L-102; Q-73 toG-101; Q-73 to A-100; Q-73 to K-99; Q-73 to P-98; Q-73 to A-97; Q-73 toG-96; Q-73 to A-95; Q-73 to G-94; Q-73 to A-93; Q-73 to P-92; Q-73 toL-91; Q-73 to K-90; Q-73 to E-89; Q-73 to A-88; Q-73 to H-87; Q-73 toH-86; Q-73 to G-85; Q-73 to Q-84; Q-73 to L-83; Q-73 to E-82; Q-73 toA-81; Q-73 to R-80; and Q-73 to L-79 of SEQ ID NO:2. Polypeptidesencoded by these polynucleotides are also encompassed by the invention.The present invention is also directed to nucleic acid moleculescomprising, or alternatively, consisting of, a polynucleotide sequenceat least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to thepolynucleotide sequence encoding the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides described above. The present inventionalso encompasses the above polynucleotide sequences fused to aheterologous polynucleotide sequence. Polypeptides encoded by thesenucleic acids and/or polynucleotide sequences are also encompassed bythe invention, as are polypeptides comprising, or alternativelyconsisting of, an amino acid sequence at least 80%, 85%, 90%, 92%, 95%,96%, 97%, 98% or 99% identical to the amino acid sequence describedabove, and polynucleotides that encode such polypeptides.

The invention also provides polypeptides having one or more amino acidsdeleted from both the amino and the carboxyl termini of the predictedextracellular domain of Neutrokine-alpha, which may be describedgenerally as having residues n²-m² of SEQ ID NO:2 where n² and m² areintegers as defined above.

In another embodiment, a nucleotide sequence encoding a polypeptideconsisting of a portion of the extracellular domain of theNeutrokine-alpha amino acid sequence encoded by the cDNA plasmidcontained in the deposit having ATCC accession no. 97768, where thisportion excludes from 1 to about 206 amino acids from the amino terminusof the extracellular domain of the amino acid sequence encoded by thecDNA plasmid contained in the deposit having ATCC accession no. 97768,or from 1 to about 206 amino acids from the carboxy terminus of theextracellular domain of the amino acid sequence encoded by the cDNAplasmid contained in the deposit having ATCC accession no. 97768, or anycombination of the above amino terminal and carboxy terminal deletions,of the entire extracellular domain of the amino acid sequence encoded bythe cDNA plasmid contained in the deposit having ATCC accession no.97768.

As mentioned above, even if deletion of one or more amino acids from theN-terminus of a polypeptide results in modification or loss of one ormore functional activities (e.g., biological activity) of thepolypeptide, other functions or biological activities may still beretained. Thus, the ability of a shortened Neutrokine-alpha mutein toinduce and/or bind to antibodies which recognize the full-length ormature forms or the extracellular domain of the polypeptide generallywill be retained when less than the majority of the residues of thefull-length or mature or extracellular domain of the polypeptide areremoved from the N-terminus. Whether a particular polypeptide lackingN-terminal residues of a complete polypeptide retains such immunologicactivities can readily be determined by routine methods described hereinand otherwise known in the art. It is not unlikely that aNeutrokine-alpha mutein with a large number of deleted N-terminal aminoacid residues may retain some functional (e.g., biological orimmunogenic) activities. In fact, peptides composed of as few as sixNeutrokine-alpha amino acid residues may often evoke an immune response.

Accordingly, the present invention further provides polypeptides havingone or more residues deleted from the amino terminus of the predictedfull-length amino acid sequence of the Neutrokine-alpha shown in SEQ IDNO:2, up to the glycine residue at position number 280 of the sequenceshown SEQ ID NO:2 and polynucleotides encoding such polypeptides. Inparticular, the present invention provides polypeptides comprising theamino acid sequence of residues n³-285 of the sequence shown in SEQ IDNO:2, where n³ is an integer in the range of the amino acid position ofamino acid residues 1 to 280 of the amino acid sequence in SEQ ID NO:2.

More in particular, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, an amino acidsequence selected from the group consisting of residues of D-2 to L-285;D-3 to L-285; S-4 to L-285; T-5 to L-285; E-6 to L-285; R-7 to L-285;E-8 to L-285; Q-9 to L-285; S-10 to L-285; R-11 to L-285; L-12 to L-285;T-13 to L-285; S-14 to L-285; C-15 to L-285; L-16 to L-285; K-17 toL-285; K-18 to L-285; R-19 to L-285; E-20 to L-285; E-21 to L-285; M-22to L-285; K-23 to L-285; L-24 to L-285; K-25 to L-285; E-26 to L-285;C-27 to L-285; V-28 to L-285; S-29 to L-285; I-30 to L-285; L-31 toL-285; P-32 to L-285; R-33 to L-285; K-34 to L-285; E-35 to L-285; S-36to L-285; P-37 to L-285; S-38 to L-285; V-39 to L-285; R-40 to L-285;S-41 to L-285; S-42 to L-285; K-43 to L-285; D-44 to L-285; G-45 toL-285; K-46 to L-285; L-47 to L-285; L-48 to L-285; A-49 to L-285; A-50to L-285; T-51 to L-285; L-52 to L-285; L-53 to L-285; L-54 to L-285;A-55 to L-285; L-56 to L-285; L-57 to L-285; S-58 to L-285; C-59 toL-285; C-60 to L-285; L-61 to L-285; T-62 to L-285; V-63 to L-285; V-64to L-285; S-65 to L-285; F-66 to L-285; Y-67 to L-285; Q-68 to L-285;V-69 to L-285; A-70 to L-285; A-71 to L-285; L-72 to L-285; Q-73 toL-285; G-74 to L-285; D-75 to L-285; L-76 to L-285; A-77 to L-285; S-78to L-285; L-79 to L-285; R-80 to L-285; A-81 to L-285; E-82 to L-285;L-83 to L-285; Q-84 to L-285; G-85 to L-285; H-86 to L-285; H-87 toL-285; A-88 to L-285; E-89 to L-285; K-90 to L-285; L-91 to L-285; P-92to L-285; A-93 to L-285; G-94 to L-285; A-95 to L-285; G-96 to L-285;A-97 to L-285; P-98 to L-285; K-99 to L-285; A-100 to L-285; G-101 toL-285; L-102 to L-285; E-103 to L-285; E-104 to L-285; A-105 to L-285;P-106 to L-285; A-107 to L-285; V-108 to L-285; T-109 to L-285; A-110 toL-285; G-111 to L-285; L-112 to L-285; K-113 to L-285; I-114 to L-285;F-115 to L-285; E-116 to L-285; P-117 to L-285; P-118 to L-285; A-119 toL-285; P-120 to L-285; G-121 to L-285; E-122 to L-285; G-123 to L-285;N-124 to L-285; S-125 to L-285; S-126 to L-285; Q-127 to L-285; N-128 toL-285; S-129 to L-285; R-130 to L-285; N-131 to L-285; K-132 to L-285;R-133 to L-285; A-134 to L-285; V-135 to L-285; Q-136 to L-285; G-137 toL-285; P-138 to L-285; E-139 to L-285; E-140 to L-285; T-141 to L-285;V-142 to L-285; T-143 to L-285; Q-144 to L-285; D-145 to L-285; C-146 toL-285; L-147 to L-285; Q-148 to L-285; L-149 to L-285; I-150 to L-285;A-151 to L-285; D-152 to L-285; S-153 to L-285; E-154 to L-285; T-155 toL-285; P-156 to L-285; T-157 to L-285; I-158 to L-285; Q-159 to L-285;K-160 to L-285; G-161 to L-285; S-162 to L-285; Y-163 to L-285; T-164 toL-285; F-165 to L-285; V-166 to L-285; P-167 to L-285; W-168 to L-285;L-169 to L-285; L-170 to L-285; S-171 to L-285; F-172 to L-285; K-173 toL-285; R-174 to L-285; G-175 to L-285; S-176 to L-285; A-177 to L-285;L-178 to L-285; E-179 to L-285; E-180 to L-285; K-181 to L-285; E-182 toL-285; N-183 to L-285; K-184 to L-285; I-185 to L-285; L-186 to L-285;V-187 to L-285; K-188 to L-285; E-189 to L-285; T-190 to L-285; G-191 toL-285; Y-192 to L-285; F-193 to L-285; F-194 to L-285; I-195 to L-285;Y-196 to L-285; G-197 to L-285; Q-198 to L-285; V-199 to L-285; L-200 toL-285; Y-201 to L-285; T-202 to L-285; D-203 to L-285; K-204 to L-285;T-205 to L-285; Y-206 to L-285; A-207 to L-285; M-208 to L-285; G-209 toL-285; H-210 to L-285; L-211 to L-285; I-212 to L-285; Q-213 to L-285;R-214 to L-285; K-215 to L-285; K-216 to L-285; V-217 to L-285; H-218 toL-285; V-219 to L-285; F-220 to L-285; G-221 to L-285; D-222 to L-285;E-223 to L-285; L-224 to L-285; S-225 to L-285; L-226 to L-285; V-227 toL-285; T-228 to L-285; L-229 to L-285; F-230 to L-285; R-231 to L-285;C-232 to L-285; I-233 to L-285; Q-234 to L-285; N-235 to L-285; M-236 toL-285; P-237 to L-285; E-238 to L-285; T-239 to L-285; L-240 to L-285;P-241 to L-285; N-242 to L-285; N-243 to L-285; S-244 to L-285; C-245 toL-285; Y-246 to L-285; S-247 to L-285; A-248 to L-285; G-249 to L-285;I-250 to L-285; A-251 to L-285; K-252 to L-285; L-253 to L-285; E-254 toL-285; E-255 to L-285; G-256 to L-285; D-257 to L-285; E-258 to L-285;L-259 to L-285; Q-260 to L-285; L-261 to L-285; A-262 to L-285; I-263 toL-285; P-264 to L-285; R-265 to L-285; E-266 to L-285; N-267 to L-285;A-268 to L-285; Q-269 to L-285; I-270 to L-285; S-271 to L-285; L-272 toL-285; D-273 to L-285; G-274 to L-285; D-275 to L-285; V-276 to L-285;T-277 to L-285; F-278 to L-285; F-279 to L-285; and G-280 to L-285 ofSEQ ID NO:2. The present application is also directed to nucleic acidmolecules comprising, or alternatively, consisting of, a polynucleotidesequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99%identical to the polynucleotide sequence encoding the Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides described above. The presentinvention also encompasses the above polynucleotide sequences fused to aheterologous polynucleotide sequence. Polypeptides encoded by thesenucleic acids and/or polynucleotide sequences are also encompassed bythe invention, as are polypeptides comprising an amino acid sequence atleast 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to theamino acid sequence described above, and polynucleotides that encodesuch polypeptides.

Also as mentioned above, even if deletion of one or more amino acidsfrom the C-terminus of a protein results in modification or loss of oneor more functional activities (e.g., biological activity) of theprotein, other functional activities may still be retained. Thus, theability of a shortened Neutrokine-alpha mutein to induce and/or bind toantibodies which recognize the complete or mature form or theextracellular domain of the polypeptide generally will be retained whenless than the majority of the residues of the complete or mature form orthe extracellular domain of the polypeptide are removed from theC-terminus. Whether a particular polypeptide lacking C-terminal residuesof a complete polypeptide retains such immunologic activities canreadily be determined by routine methods described herein and otherwiseknown in the art. It is not unlikely that a Neutrokine-alpha mutein witha large number of deleted C-terminal amino acid residues may retain somefunctional (e.g., biological or immunogenic) activities. In fact,peptides composed of as few as six Neutrokine-alpha amino acid residuesmay often evoke an immune response.

Accordingly, the present invention further provides in anotherembodiment, polypeptides having one or more residues deleted from thecarboxy terminus of the amino acid sequence of the Neutrokine-alphashown in SEQ ID NO:2, up to the glutamic acid residue at position number6, and polynucleotides encoding such polypeptides. In particular, thepresent invention provides polypeptides comprising the amino acidsequence of residues 1-m³ of SEQ ID NO:2, where m³ is an integer in therange of the amino acid position of amino acid residues 6-284 of theamino acid sequence in SEQ ID NO:2.

More in particular, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, an amino acidsequence selected from the group consisting of residues M-1 to L-284;M-1 to K-283; M-1 to L-282; M-1 to A-281; M-1 to G-280; M-1 to F-279;M-1 to F-278; M-1 to T-277; M-1 to V-276; M-1 to D-275; M-1 to G-274;M-1 to D-273; M-1 to L-272; M-1 to S-271; M-1 to I-270; M-1 to Q-269;M-1 to A-268; M-1 to N-267; M-1 to E-266; M-1 to R-265; M-1 to P-264;M-1 to I-263; M-1 to A-262; M-1 to L-261; M-1 to Q-260; M-1 to L-259;M-1 to E-258; M-1 to D-257; M-1 to G-256; M-1 to E-255; M-1 to E-254;M-1 to L-253; M-1 to K-252; M-1 to A-251; M-1 to I-250; M-1 to G-249;M-1 to A-248; M-1 to S-247; M-1 to Y-246; M-1 to C-245; M-1 to S-244;M-1 to N-243; M-1 to N-242; M-1 to P-241; M-1 to L-240; M-1 to T-239;M-1 to E-238; M-1 to P-237; M-1 to M-236; M-1 to N-235; M-1 to Q-234;M-1 to I-233; M-1 to C-232; M-1 to R-231; M-1 to F-230; M-1 to L-229;M-1 to T-228; M-1 to V-227; M-1 to L-226; M-1 to S-225; M-1 to L-224;M-1 to E-223; M-1 to D-222; M-1 to G-221; M-1 to F-220; M-1 to V-219;M-1 to H-218; M-1 to V-217; M-1 to K-216; M-1 to K-215; M-1 to R-214;M-1 to Q-213; M-1 to I-212; M-1 to L-211; M-1 to H-210; M-1 to G-209;M-1 to M-208; M-1 to A-207; M-1 to Y-206; M-1 to T-205; M-1 to K-204;M-1 to D-203; M-1 to T-202; M-1 to Y-201; M-1 to L-200; M-1 to V-199;M-1 to Q-198; M-1 to G-197; M-1 to Y-196; M-1 to I-195; M-1 to F-194;M-1 to F-193; M-1 to Y-192; M-1 to G-191; M-1 to T-190; M-1 to E-189;M-1 to K-188; M-1 to V-187; M-1 to L-186; M-1 to I-185; M-1 to K-184;M-1 to N-183; M-1 to E-182; M-1 to K-181; M-1 to E-180; M-1 to E-179;M-1 to L-178; M-1 to A-177; M-1 to S-176; M-1 to G-175; M-1 to R-174;M-1 to K-173; M-1 to F-172; M-1 to S-171; M-1 to L-170; M-1 to L-169;M-1 to W-168; M-1 to P-167; M-1 to V-166; M-1 to F-165; M-1 to T-164;M-1 to Y-163; M-1 to S-162; M-1 to G-161; M-1 to K-160; M-1 to Q-159;M-1 to I-158; M-1 to T-157; M-1 to P-156; M-1 to T-155; M-1 to E-154;M-1 to S-153; M-1 to D-152; M-1 to A-151; M-1 to I-150; M-1 to L-149;M-1 to Q-148; M-1 to L-147; M-1 to C-146; M-1 to D-145; M-1 to Q-144;M-1 to T-143; M-1 to V-142; M-1 to T-141; M-1 to E-140; M-1 to E-139;M-1 to P-138; M-1 to G-137; M-1 to Q-136; M-1 to V-135; M-1 to A-134;M-1 to R-133; M-1 to K-132; M-1 to N-131; M-1 to R-130; M-1 to S-129;M-1 to N-128; M-1 to Q-127; M-1 to S-126; M-1 to S-125; M-1 to N-124;M-1 to G-123; M-1 to E-122; M-1 to G-121; M-1 to P-120; M-1 to A-119;M-1 to P-118; M-1 to P-117; M-1 to E-116; M-1 to F-115; M-1 to I-114;M-1 to K-113; M-1 to L-112; M-1 to G-111; M-1 to A-110; M-1 to T-109;M-1 to V-108; M-1 to A-107; M-1 to P-106; M-1 to A-105; M-1 to E-104;M-1 to E-103; M-1 to L-102; M-1 to G-101; M-1 to A-100; M-1 to K-99; M-1to P-98; M-1 to A-97; M-1 to G-96; M-1 to A-95; M-1 to G-94; M-1 toA-93; M-1 to P-92; M-1 to L-91; M-1 to K-90; M-1 to E-89; M-1 to A-88;M-1 to H-87; M-1 to H-86; M-1 to G-85; M-1 to Q-84; M-1 to L-83; M-1 toE-82; M-1 to A-81; M-1 to R-80; M-1 to L-79; M-1 to S-78; M-1 to A-77;M-1 to L-76; M-1 to D-75; M-1 to G-74; M-1 to Q-73; M-1 to L-72; M-1 toA-71; M-1 to A-70; M-1 to V-69; M-1 to Q-68; M-1 to Y-67; M-1 to F-66;M-1 to S-65; M-1 to V-64; M-1 to V-63; M-1 to T-62; M-1 to L-61; M-1 toC-60; M-1 to C-59; M-1 to S-58; M-1 to L-57; M-1 to L-56; M-1 to A-55;M-1 to L-54; M-1 to L-53; M-1 to L-52; M-1 to T-51; M-1 to A-50; M-1 toA-49; M-1 to L-48; M-1 to L-47; M-1 to K-46; M-1 to G-45; M-1 to D-44;M-1 to K-43; M-1 to S-42; M-1 to S-41; M-1 to R-40; M-1 to V-39; M-1 toS-38; M-1 to P-37; M-1 to S-36; M-1 to E-35; M-1 to K-34; M-1 to R-33;M-1 to P-32; M-1 to L-31; M-1 to I-30; M-1 to S-29; M-1 to V-28; M-1 toC-27; M-1 to E-26; M-1 to K-25; M-1 to L-24; M-1 to K-23; M-1 to M-22;M-1 to E-21; M-1 to E-20; M-1 to R-19; M-1 to K-18; M-1 to K-17; M-1 toL-16; M-1 to C-15; M-1 to S-14; M-1 to T-13; M-1 to L-12; M-1 to R-11;M-1 to S-10; M-1 to Q-9; M-1 to E-8; M-1 to R-7; and M-1 to E-6 of SEQID NO:2. The present application is also directed to nucleic acidmolecules comprising, or alternatively, consisting of, a polynucleotidesequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99%identical to the polynucleotide sequence encoding the Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides described above. The presentinvention also encompasses the above polynucleotide sequences fused to aheterologous polynucleotide sequence. Polypeptides encoded by thesenucleic acids and/or polynucleotide sequences are also encompassed bythe invention, as are polypeptides comprising an amino acid sequence atleast 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to theamino acid sequence described above, and polynucleotides that encodesuch polypeptides.

The invention also provides polypeptides having one or more amino acidsdeleted from both the amino and the carboxyl termini of aNeutrokine-alpha polypeptide, which may be described generally as havingresidues n³-m³ of SEQ ID NO:2, where n³ and m³ are integers as definedabove.

Furthermore, since the predicted extracellular domain of theNeutrokine-alphaSV polypeptides of the invention may itself elicitfunctional activity (e.g., biological activity), deletions of N- andC-terminal amino acid residues from the predicted extracellular regionof the polypeptide at positions Gln-73 to Leu-266 of SEQ ID NO:19 mayretain some functional activity, such as, for example, ligand binding,to stimulation of lymphocyte (e.g., B cell) proliferation,differentiation, and/or activation, modulation of cell replication,modulation of target cell activities and/or immunogenicity. However,even if deletion of one or more amino acids from the N-terminus of thepredicted extracellular domain of a Neutrokine-alphaSV polypeptideresults in modification or loss of one or more functional activities ofthe polypeptide, other functional activities may still be retained.Thus, the ability of the shortened polypeptides to induce and/or bind toantibodies which recognize the complete or mature or extracellulardomains of the polypeptides generally will be retained when less thanthe majority of the residues of the complete or mature or extracellulardomains of the polypeptides are removed from the N-terminus. Whether aparticular polypeptide lacking N-terminal residues of a completepolypeptide retains such immunologic activities can readily bedetermined by routine methods described herein and otherwise known inthe art.

Accordingly, the present invention further provides polypeptides havingone or more residues deleted from the amino terminus of the amino acidsequence of Neutrokine-alphaSV shown in SEQ ID NO:19, up to the glycineresidue at position number 261, and polynucleotides encoding suchpolypeptides. In particular, the present invention provides polypeptidescomprising the amino acid sequence of residues n⁴-266 of SEQ ID NO:19,where n⁴ is an integer in the range of the amino acid position of aminoacid residues 73-261 of the amino acid sequence in SEQ ID NO:19, and 261is the position of the first residue from the N-terminus of thepredicted extracellular domain Neutrokine-alphaSV polypeptide (shown inSEQ ID NO:19).

More in particular, in certain embodiments, the invention providespolynucleotides encoding polypeptides comprising, or alternativelyconsisting of, an amino acid sequence selected from the group consistingof residues of Q-73 to L-266; G-74 to L-266; D-75 to L-266; L-76 toL-266; A-77 to L-266; S-78 to L-266; L-79 to L-266; R-80 to L-266; A-81to L-266; E-82 to L-266; L-83 to L-266; Q-84 to L-266; G-85 to L-266;H-86 to L-266; H-87 to L-266; A-88 to L-266; E-89 to L-266; K-90 toL-266; L-91 to L-266; P-92 to L-266; A-93 to L-266; G-94 to L-266; A-95to L-266; G-96 to L-266; A-97 to L-266; P-98 to L-266; K-99 to L-266;A-100 to L-266; G-101 to L-266; L-102 to L-266; E-103 to L-266; E-104 toL-266; A-105 to L-266; P-106 to L-266; A-107 to L-266; V-108 to L-266;T-109 to L-266; A-110 to L-266; G-111 to L-266; L-112 to L-266; K-113 toL-266; I-114 to L-266; F-115 to L-266; E-116 to L-266; P-117 to L-266;P-118 to L-266; A-119 to L-266; P-120 to L-266; G-121 to L-266; E-122 toL-266; G-123 to L-266; N-124 to L-266; S-125 to L-266; S-126 to L-266;Q-127 to L-266; N-128 to L-266; S-129 to L-266; R-130 to L-266; N-131 toL-266; K-132 to L-266; R-133 to L-266; A-134 to L-266; V-135 to L-266;Q-136 to L-266; G-137 to L-266; P-138 to L-266; E-139 to L-266; E-140 toL-266; T-141 to L-266; G-142 to L-266; S-143 to L-266; Y-144 to L-266;T-145 to L-266; F-146 to L-266; V-147 to L-266; P-148 to L-266; W-149 toL-266; L-150 to L-266; L-151 to L-266; S-152 to L-266; F-153 to L-266;K-154 to L-266; R-155 to L-266; G-156 to L-266; S-157 to L-266; A-158 toL-266; L-159 to L-266; E-160 to L-266; E-161 to L-266; K-162 to L-266;E-163 to L-266; N-164 to L-266; K-165 to L-266; I-166 to L-266; L-167 toL-266; V-168 to L-266; K-169 to L-266; E-170 to L-266; T-171 to L-266;G-172 to L-266; Y-173 to L-266; F-174 to L-266; F-175 to L-266; I-176 toL-266; Y-177 to L-266; G-178 to L-266; Q-179 to L-266; V-180 to L-266;L-181 to L-266; Y-182 to L-266; T-183 to L-266; D-184 to L-266; K-185 toL-266; T-186 to L-266; Y-187 to L-266; A-188 to L-266; M-189 to L-266;G-190 to L-266; H-191 to L-266; L-192 to L-266; I-193 to L-266; Q-194 toL-266; R-195 to L-266; K-196 to L-266; K-197 to L-266; V-198 to L-266;H-199 to L-266; V-200 to L-266; F-201 to L-266; G-202 to L-266; D-203 toL-266; E-204 to L-266; L-205 to L-266; S-206 to L-266; L-207 to L-266;V-208 to L-266; T-209 to L-266; L-210 to L-266; F-211 to L-266; R-212 toL-266; C-213 to L-266; I-214 to L-266; Q-215 to L-266; N-216 to L-266;M-217 to L-266; P-218 to L-266; E-219 to L-266; T-220 to L-266; L-221 toL-266; P-222 to L-266; N-223 to L-266; N-224 to L-266; S-225 to L-266;C-226 to L-266; Y-227 to L-266; S-228 to L-266; A-229 to L-266; G-230 toL-266; I-231 to L-266; A-232 to L-266; K-233 to L-266; L-234 to L-266;E-235 to L-266; E-236 to L-266; G-237 to L-266; D-238 to L-266; E-239 toL-266; L-240 to L-266; Q-241 to L-266; L-242 to L-266; A-243 to L-266;I-244 to L-266; P-245 to L-266; R-246 to L-266; E-247 to L-266; N-248 toL-266; A-249 to L-266; Q-250 to L-266; I-251 to L-266; S-252 to L-266;L-253 to L-266; D-254 to L-266; G-255 to L-266; D-256 to L-266; V-257 toL-266; T-258 to L-266; F-259 to L-266; F-260 to L-266; and G-261 toL-266 of SEQ ID NO:19. The present application is also directed tonucleic acid molecules comprising, or alternatively, consisting of, apolynucleotide sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%or 99% identical to the polynucleotide sequence encoding theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides described above.The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these nucleic acids and/or polynucleotide sequences are alsoencompassed by the invention, as are polypeptides comprising an aminoacid sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99%identical to the amino acid sequence described above, andpolynucleotides that encode such polypeptides.

Similarly, deletions of C-terminal amino acid residues of the predictedextracellular domain of Neutrokine-alphaSV up to the leucine residue atposition 79 of SEQ ID NO:19 may retain some functional activity, suchas, for example, ligand binding, the ability to stimulate lymphocyte(e.g., B cell) proliferation, differentiation, and/or activation,modulation of cell replication, modulation of target cell activitiesand/or immunogenicity. Polypeptides having further C-terminal deletionsincluding Leu-79 of SEQ ID NO:19 would not be expected to retainbiological activities.

However, even if deletion of one or more amino acids from the C-terminusof a polypeptide results in modification or loss of one or morefunctional activities (e.g., biological activity) of the polypeptide,other functional activities may still be retained. Thus, the ability ofthe shortened polypeptide to induce and/or bind to antibodies whichrecognize the complete, mature or extracellular forms of the polypeptidegenerally will be retained when less than the majority of the residuesof the complete, mature or extracellular forms of the polypeptide areremoved from the C-terminus. Whether a particular polypeptide lackingC-terminal residues of the predicted extracellular domain retains suchimmunologic activities can readily be determined by routine methodsdescribed herein and otherwise known in the art.

Accordingly, the present invention further provides polypeptides havingone or more residues from the carboxy terminus of the amino acidsequence of the predicted extracellular domain of Neutrokine-alphaSVshown in SEQ ID NO:19, up to the leucine residue at position 79 of SEQID NO:19, and polynucleotides encoding such polypeptides. In particular,the present invention provides polypeptides having the amino acidsequence of residues 73-m⁴ of the amino acid sequence in SEQ ID NO:19,where m⁴ is any integer in the range of the amino acid position of aminoacid residues 79-266 of the amino acid sequence in SEQ ID NO:19.

More in particular, in certain embodiments, the invention providespolynucleotides encoding polypeptides comprising, or alternativelyconsisting of, an amino acid sequence selected from the group consistingof residues Q-73 to L-265; Q-73 to K-264; Q-73 to L-263; Q-73 to A-262;Q-73 to G-261; Q-73 to F-260; Q-73 to F-259; Q-73 to T-258; Q-73 toV-257; Q-73 to D-256; Q-73 to G-255; Q-73 to D-254; Q-73 to L-253; Q-73to S-252; Q-73 to I-251; Q-73 to Q-250; Q-73 to A-249; Q-73 to N-248;Q-73 to E-247; Q-73 to R-246; Q-73 to P-245; Q-73 to I-244; Q-73 toA-243; Q-73 to L-242; Q-73 to Q-241; Q-73 to L-240; Q-73 to E-239; Q-73to D-238; Q-73 to G-237; Q-73 to E-236; Q-73 to E-235; Q-73 to L-234;Q-73 to K-233; Q-73 to A-232; Q-73 to I-231; Q-73 to G-230; Q-73 toA-229; Q-73 to S-228; Q-73 to Y-227; Q-73 to C-226; Q-73 to S-225; Q-73to N-224; Q-73 to N-223; Q-73 to P-222; Q-73 to L-221; Q-73 to T-220;Q-73 to E-219; Q-73 to P-218; Q-73 to M-217; Q-73 to N-216; Q-73 toQ-215; Q-73 to I-214; Q-73 to C-213; Q-73 to R-212; Q-73 to F-211; Q-73to L-210; Q-73 to T-209; Q-73 to V-208; Q-73 to L-207; Q-73 to S-206;Q-73 to L-205; Q-73 to E-204; Q-73 to D-203; Q-73 to G-202; Q-73 toF-201; Q-73 to V-200; Q-73 to H-199; Q-73 to V-198; Q-73 to K-197; Q-73to K-196; Q-73 to R-195; Q-73 to Q-194; Q-73 to I-193; Q-73 to L-192;Q-73 to H-191; Q-73 to G-190; Q-73 to Q-7389; Q-73 to A-188; Q-73 toY-187; Q-73 to T-186; Q-73 to K-185; Q-73 to D-184; Q-73 to T-183; Q-73to Y-182; Q-73 to L-181; Q-73 to V-180; Q-73 to Q-179; Q-73 to G-178;Q-73 to Y-177; Q-73 to I-176; Q-73 to F-175; Q-73 to F-174; Q-73 toY-173; Q-73 to G-172; Q-73 to T-171; Q-73 to E-170; Q-73 to K-169; Q-73to V-168; Q-73 to L-167; Q-73 to I-166; Q-73 to K-165; Q-73 to N-164;Q-73 to E-163; Q-73 to K-162; Q-73 to E-161; Q-73 to E-160; Q-73 toL-159; Q-73 to A-158; Q-73 to S-157; Q-73 to G-156; Q-73 to R-155; Q-73to K-154; Q-73 to F-153; Q-73 to S-152; Q-73 to L-151; Q-73 to L-150;Q-73 to W-149; Q-73 to P-148; Q-73 to V-147; Q-73 to F-146; Q-73 toT-145; Q-73 to Y-144; Q-73 to S-143; Q-73 to G-142; Q-73 to T-141; Q-73to E-140; Q-73 to E-139; Q-73 to P-138; Q-73 to G-137; Q-73 to Q-136;Q-73 to V-135; Q-73 to A-134; Q-73 to R-133; Q-73 to K-132; Q-73 toN-131; Q-73 to R-130; Q-73 to S-129; Q-73 to N-128; Q-73 to Q-127; Q-73to S-126; Q-73 to S-125; Q-73 to N-124; Q-73 to G-123; Q-73 to E-122;Q-73 to G-121; Q-73 to P-120; Q-73 to A-119; Q-73 to P-118; Q-73 toP-117; Q-73 to E-116; Q-73 to F-115; Q-73 to I-114; Q-73 to K-113; Q-73to L-112; Q-73 to G-111; Q-73 to A-110; Q-73 to T-109; Q-73 to V-108;Q-73 to A-107; Q-73 to P-106; Q-73 to A-105; Q-73 to E-104; Q-73 toE-103; Q-73 to L-102; Q-73 to G-101; Q-73 to A-100; Q-73 to K-99; Q-73to P-98; Q-73 to A-97; Q-73 to G-96; Q-73 to A-95; Q-73 to G-94; Q-73 toA-93; Q-73 to P-92; Q-73 to L-91; Q-73 to K-90; Q-73 to E-89; Q-73 toA-88; Q-73 to H-87; Q-73 to H-86; Q-73 to G-85; Q-73 to Q-84; Q-73 toL-83; Q-73 to E-82; Q-73 to A-81; Q-73 to R-80; Q-73 to L-79; and Q-73to S-78 of SEQ ID NO:19. The present application is also directed tonucleic acid molecules comprising, or alternatively, consisting of, apolynucleotide sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%or 99% identical to the polynucleotide sequence encoding theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides described above.The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these nucleic acids and/or polynucleotide sequences are alsoencompassed by the invention, as are polypeptides comprising an aminoacid sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99%identical to the amino acid sequence described above, andpolynucleotides that encode such polypeptides.

The invention also provides polypeptides having one or more amino acidsdeleted from both the amino and the carboxyl termini of the predictedextracellular domain of Neutrokine-alphaSV, which may be describedgenerally as having residues n⁴-m⁴ of SEQ ID NO:19 where n⁴ and m⁴ areintegers as defined above.

In another embodiment, a nucleotide sequence encoding a polypeptideconsisting of a portion of the extracellular domain of theNeutrokine-alphaSV amino acid sequence encoded by the cDNA clonecontained in the deposit having ATCC Accession No. 203518, where thisportion excludes from 1 to about 260 amino acids from the amino terminusof the extracellular domain of the amino acid sequence encoded by cDNAclone contained in the deposit having ATCC Accession No. 203518, or from1 to about 187 amino acids from the carboxy terminus of theextracellular domain of the amino acid sequence encoded by cDNA clonecontained in the deposit having ATCC Accession No. 203518, or anycombination of the above amino terminal and carboxy terminal deletions,of the entire extracellular domain of the amino acid sequence encoded bythe cDNA clone contained in the deposit having ATCC Accession No.203518.

As mentioned above, even if deletion of one or more amino acids from theN-terminus of a polypeptide results in modification or loss of one ormore functional activities (e.g., biological activity) of thepolypeptide, other functional activities may still be retained. Thus,the ability of a shortened Neutrokine-alphaSV mutein to induce and/orbind to antibodies which recognize the full-length or mature forms orthe extracellular domain of the polypeptide generally will be retainedwhen less than the majority of the residues of the full-length or matureor extracellular domain of the polypeptide are removed from theN-terminus. Whether a particular polypeptide lacking N-terminal residuesof a complete polypeptide retains such immunologic activities canreadily be determined by routine methods described herein and otherwiseknown in the art. It is not unlikely that a Neutrokine-alphaSV muteinwith a large number of deleted N-terminal amino acid residues may retainfunctional (e.g., immunogenic) activities. In fact, peptides composed ofas few as six Neutrokine-alphaSV amino acid residues may often evoke animmune response.

Accordingly, the present invention further provides polypeptides havingone or more residues deleted from the amino terminus of the predictedfull-length amino acid sequence of the Neutrokine-alphaSV shown in SEQID NO:19, up to the glycine residue at position number 261 of thesequence shown SEQ ID NO:19 and polynucleotides encoding suchpolypeptides. In particular, the present invention provides polypeptidescomprising the amino acid sequence of residues n⁵-266 of the sequenceshown in SEQ ID NO:19, where n⁵ is an integer in the range of the aminoacid position of amino acid residues 1 to 261 of the amino acid sequencein SEQ ID NO:19.

More in particular, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, an amino acidsequence selected from the group consisting of residues of D-2 to L-266;D-3 to L-266; S-4 to L-266; T-5 to L-266; E-6 to L-266; R-7 to L-266;E-8 to L-266; Q-9 to L-266; S-10 to L-266; R-11 to L-266; L-12 to L-266;T-13 to L-266; S-14 to L-266; C-15 to L-266; L-16 to L-266; K-17 toL-266; K-18 to L-266; R-19 to L-266; E-20 to L-266; E-21 to L-266; M-22to L-266; K-23 to L-266; L-24 to L-266; K-25 to L-266; E-26 to L-266;C-27 to L-266; V-28 to L-266; S-29 to L-266; I-30 to L-266; L-31 toL-266; P-32 to L-266; R-33 to L-266; K-34 to L-266; E-35 to L-266; S-36to L-266; P-37 to L-266; S-38 to L-266; V-39 to L-266; R-40 to L-266;S-41 to L-266; S-42 to L-266; K-43 to L-266; D-44 to L-266; G-45 toL-266; K-46 to L-266; L-47 to L-266; L-48 to L-266; A-49 to L-266; A-50to L-266; T-51 to L-266; L-52 to L-266; L-53 to L-266; L-54 to L-266;A-55 to L-266; L-56 to L-266; L-57 to L-266; S-58 to L-266; C-59 toL-266; C-60 to L-266; L-61 to L-266; T-62 to L-266; V-63 to L-266; V-64to L-266; S-65 to L-266; F-66 to L-266; Y-67 to L-266; Q-68 to L-266;V-69 to L-266; A-70 to L-266; A-71 to L-266; L-72 to L-266; Q-73 toL-266; G-74 to L-266; D-75 to L-266; L-76 to L-266; A-77 to L-266; S-78to L-266; L-79 to L-266; R-80 to L-266; A-81 to L-266; E-82 to L-266;L-83 to L-266; Q-84 to L-266; G-85 to L-266; H-86 to L-266; H-87 toL-266; A-88 to L-266; E-89 to L-266; K-90 to L-266; L-91 to L-266; P-92to L-266; A-93 to L-266; G-94 to L-266; A-95 to L-266; G-96 to L-266;A-97 to L-266; P-98 to L-266; K-99 to L-266; A-100 to L-266; G-101 toL-266; L-102 to L-266; E-103 to L-266; E-104 to L-266; A-105 to L-266;P-106 to L-266; A-107 to L-266; V-108 to L-266; T-109 to L-266; A-110 toL-266; G-111 to L-266; L-112 to L-266; K-113 to L-266; I-114 to L-266;F-115 to L-266; E-116 to L-266; P-117 to L-266; P-118 to L-266; A-119 toL-266; P-120 to L-266; G-121 to L-266; E-122 to L-266; G-123 to L-266;N-124 to L-266; S-125 to L-266; S-126 to L-266; Q-127 to L-266; N-128 toL-266; S-129 to L-266; R-130 to L-266; N-131 to L-266; K-132 to L-266;R-133 to L-266; A-134 to L-266; V-135 to L-266; Q-136 to L-266; G-137 toL-266; P-138 to L-266; E-139 to L-266; E-140 to L-266; T-141 to L-266;G-142 to L-266; S-143 to L-266; Y-144 to L-266; T-145 to L-266; F-146 toL-266; V-147 to L-266; P-148 to L-266; W-149 to L-266; L-150 to L-266;L-151 to L-266; S-152 to L-266; F-153 to L-266; K-154 to L-266; R-155 toL-266; G-156 to L-266; S-157 to L-266; A-158 to L-266; L-159 to L-266;E-160 to L-266; E-161 to L-266; K-162 to L-266; E-163 to L-266; N-164 toL-266; K-165 to L-266; I-166 to L-266; L-167 to L-266; V-168 to L-266;K-169 to L-266; E-170 to L-266; T-171 to L-266; G-172 to L-266; Y-173 toL-266; F-174 to L-266; F-175 to L-266; I-176 to L-266; Y-177 to L-266;G-178 to L-266; Q-179 to L-266; V-180 to L-266; L-181 to L-266; Y-182 toL-266; T-183 to L-266; D-184 to L-266; K-185 to L-266; T-186 to L-266;Y-187 to L-266; A-188 to L-266; M-189 to L-266; G-190 to L-266; H-191 toL-266; L-192 to L-266; I-193 to L-266; Q-194 to L-266; R-195 to L-266;K-196 to L-266; K-197 to L-266; V-198 to L-266; H-199 to L-266; V-200 toL-266; F-201 to L-266; G-202 to L-266; D-203 to L-266; E-204 to L-266;L-205 to L-266; S-206 to L-266; L-207 to L-266; V-208 to L-266; T-209 toL-266; L-210 to L-266; F-211 to L-266; R-212 to L-266; C-213 to L-266;I-214 to L-266; Q-215 to L-266; N-216 to L-266; M-217 to L-266; P-218 toL-266; E-219 to L-266; T-220 to L-266; L-221 to L-266; P-222 to L-266;N-223 to L-266; N-224 to L-266; S-225 to L-266; C-226 to L-266; Y-227 toL-266; S-228 to L-266; A-229 to L-266; G-230 to L-266; I-231 to L-266;A-232 to L-266; K-233 to L-266; L-234 to L-266; E-235 to L-266; E-236 toL-266; G-237 to L-266; D-238 to L-266; E-239 to L-266; L-240 to L-266;Q-241 to L-266; L-242 to L-266; A-243 to L-266; I-244 to L-266; P-245 toL-266; R-246 to L-266; E-247 to L-266; N-248 to L-266; A-249 to L-266;Q-250 to L-266; I-251 to L-266; S-252 to L-266; L-253 to L-266; D-254 toL-266; G-255 to L-266; D-256 to L-266; V-257 to L-266; T-258 to L-266;F-259 to L-266; F-260 to L-266; and G-261 to L-266 of SEQ ID NO:19. Thepresent application is also directed to nucleic acid moleculescomprising, or alternatively, consisting of, a polynucleotide sequenceat least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to thepolynucleotide sequence encoding the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides described above. The present inventionalso encompasses the above polynucleotide sequences fused to aheterologous polynucleotide sequence. Polypeptides encoded by thesenucleic acids and/or polynucleotide sequences are also encompassed bythe invention, as are polypeptides comprising an amino acid sequence atleast 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to theamino acid sequence described above, and polynucleotides that encodesuch polypeptides.

Also as mentioned above, even if deletion of one or more amino acidsfrom the C-terminus of a protein results in modification or loss of oneor more functional activities (e.g., biological activities) of theprotein, other functional activities may still be retained. Thus, theability of a shortened Neutrokine-alphaSV mutein to induce and/or bindto antibodies which recognize the complete or mature form or theextracellular domain of the polypeptide generally will be retained whenless than the majority of the residues of the complete or mature form orthe extracellular domain of the polypeptide are removed from theC-terminus. Whether a particular polypeptide lacking C-terminal residuesof a complete polypeptide retains such immunologic activities canreadily be determined by routine methods described herein and otherwiseknown in the art. It is not unlikely that a Neutrokine-alphaSV muteinwith a large number of deleted C-terminal amino acid residues may retainsome functional (e.g., immunogenic) activities. In fact, peptidescomposed of as few as six Neutrokine-alphaSV amino acid residues mayoften evoke an immune response.

Accordingly, the present invention further provides in anotherembodiment, polypeptides having one or more residues deleted from thecarboxy terminus of the amino acid sequence of the Neutrokine-alphaSVshown in SEQ ID NO:19, up to the glutamic acid residue at positionnumber 6, and polynucleotides encoding such polypeptides. In particular,the present invention provides polypeptides comprising the amino acidsequence of residues 1-m⁵ of SEQ ID NO:19, where m⁵ is an integer in therange of the amino acid position of amino acid residues 6 to 265 in theamino acid sequence of SEQ ID NO:19.

More in particular, the invention provides polynucleotides encodingpolypeptides comprising, or alternatively consisting of, an amino acidsequence selected from the group consisting of residues M-1 to L-265;M-1 to K-264; M-1 to L-263; M-1 to A-262; M-1 to G-261; M-1 to F-260;M-1 to F-259; M-1 to T-258; M-1 to V-257; M-1 to D-256; M-1 to G-255;M-1 to D-254; M-1 to L-253; M-1 to S-252; M-1 to I-251; M-1 to Q-250;M-1 to A-249; M-1 to N-248; M-1 to E-247; M-1 to R-246; M-1 to P-245;M-1 to I-244; M-1 to A-243; M-1 to L-242; M-1 to Q-241; M-1 to L-240;M-1 to E-239; M-1 to D-238; M-1 to G-237; M-1 to E-236; M-1 to E-235;M-1 to L-234; M-1 to K-233; M-1 to A-232; M-1 to I-231; M-1 to G-230;M-1 to A-229; M-1 to S-228; M-1 to Y-227; M-1 to C-226; M-1 to S-225;M-1 to N-224; M-1 to N-223; M-1 to P-222; M-1 to L-221; M-1 to T-220;M-1 to E-219; M-1 to P-218; M-1 to M-217; M-1 to N-216; M-1 to Q-215;M-1 to I-214; M-1 to C-213; M-1 to R-212; M-1 to F-211; M-1 to L-210;M-1 to T-209; M-1 to V-208; M-1 to L-207; M-1 to S-206; M-1 to L-205;M-1 to E-204; M-1 to D-203; M-1 to G-202; M-1 to F-201; M-1 to V-200;M-1 to H-199; M-1 to V-198; M-1 to K-197; M-1 to K-196; M-1 to R-195;M-1 to Q-194; M-1 to I-193; M-1 to L-192; M-1 to H-191; M-1 to G-190;M-1 to M-189; M-1 to A-188; M-1 to Y-187; M-1 to T-186; M-1 to K-185;M-1 to D-184; M-1 to T-183; M-1 to Y-182; M-1 to L-181; M-1 to V-180;M-1 to Q-179; M-1 to G-178; M-1 to Y-177; M-1 to I-176; M-1 to F-175;M-1 to F-174; M-1 to Y-173; M-1 to G-172; M-1 to T-171; M-1 to E-170;M-1 to K-169; M-1 to V-168; M-1 to L-167; M-1 to I-166; M-1 to K-165;M-1 to N-164; M-1 to E-163; M-1 to K-162; M-1 to E-161; M-1 to E-160;M-1 to L-159; M-1 to A-158; M-1 to S-157; M-1 to G-156; M-1 to R-155;M-1 to K-154; M-1 to F-153; M-1 to S-152; M-1 to L-151; M-1 to L-150;M-1 to W-149; M-1 to P-148; M-1 to V-147; M-1 to F-146; M-1 to T-145;M-1 to Y-144; M-1 to S-143; M-1 to G-142; M-1 to T-141; M-1 to E-140;M-1 to E-139; M-1 to P-138; M-1 to G-137; M-1 to Q-136; M-1 to V-135;M-1 to A-134; M-1 to R-133; M-1 to K-132; M-1 to N-131; M-1 to R-130;M-1 to S-129; M-1 to N-128; M-1 to Q-127; M-1 to S-126; M-1 to S-125;M-1 to N-124; M-1 to G-123; M-1 to E-122; M-1 to G-121; M-1 to P-120;M-1 to A-119; M-1 to P-118; M-1 to P-117; M-1 to E-116; M-1 to F-115;M-1 to I-114; M-1 to K-113; M-1 to L-112; M-1 to G-111; M-1 to A-110;M-1 to T-109; M-1 to V-108; M-1 to A-107; M-1 to P-106; M-1 to A-105;M-1 to E-104; M-1 to E-103; M-1 to L-102; M-1 to G-101; M-1 to A-100;M-1 to K-99; M-1 to P-98; M-1 to A-97; M-1 to G-96; M-1 to A-95; M-1 toG-94; M-1 to A-93; M-1 to P-92; M-1 to L-91; M-1 to K-90; M-1 to E-89;M-1 to A-88; M-1 to H-87; M-1 to H-86; M-1 to G-85; M-1 to Q-84; M-1 toL-83; M-1 to E-82; M-1 to A-81; M-1 to R-80; M-1 to L-79; M-1 to S-78;M-1 to A-77; M-1 to L-76; M-1 to D-75; M-1 to G-74; M-1 to Q-73; M-1 toL-72; M-1 to A-71; M-1 to A-70; M-1 to V-69; M-1 to Q-68; M-1 to Y-67;M-1 to F-66; M-1 to S-65; M-1 to V-64; M-1 to V-63; M-1 to T-62; M-1 toL-61; M-1 to C-60; M-1 to C-59; M-1 to S-58; M-1 to L-57; M-1 to L-56;M-1 to A-55; M-1 to L-54; M-1 to L-53; M-1 to L-52; M-1 to T-51; M-1 toA-50; M-1 to A-49; M-1 to L-48; M-1 to L-47; M-1 to K-46; M-1 to G-45;M-1 to D-44; M-1 to K-43; M-1 to S-42; M-1 to S-41; M-1 to R-40; M-1 toV-39; M-1 to S-38; M-1 to P-37; M-1 to S-36; M-1 to E-35; M-1 to K-34;M-1 to R-33; M-1 to P-32; M-1 to L-31; M-1 to I-30; M-1 to S-29; M-1 toV-28; M-1 to C-27; M-1 to E-26; M-1 to K-25; M-1 to L-24; M-1 to K-23;M-1 to M-22; M-1 to E-21; M-1 to E-20; M-1 to R-19; M-1 to K-18; M-1 toK-17; M-1 to L-16; M-1 to C-15; M-1 to S-14; M-1 to T-13; M-1 to L-12;M-1 to R-11; M-1 to S-10; M-1 to Q-9; M-1 to E-8; M-1 to R-7; and M-1 toE-6 of SEQ ID NO:19. The present application is also directed to nucleicacid molecules comprising, or alternatively, consisting of, apolynucleotide sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98%or 99% identical to the polynucleotide sequence encoding theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides described above.The present invention also encompasses the above polynucleotidesequences fused to a heterologous polynucleotide sequence. Polypeptidesencoded by these nucleic acids and/or polynucleotide sequences are alsoencompassed by the invention, as are polypeptides comprising an aminoacid sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99%identical to the amino acid sequence described above, andpolynucleotides that encode such polypeptides.

The invention also provides polypeptides having one or more amino acidsdeleted from both the amino and the carboxyl termini of aNeutrokine-alphaSV polypeptide, which may be described generally ashaving residues n⁵-m⁵ of SEQ ID NO:19, where n⁵ and m⁵ are integers asdefined above.

In additional embodiments, the present invention provides polypeptidescomprising the amino acid sequence of residues 134-m⁶ of SEQ ID NO:2,where m⁶ is an integer from 140 to 285, corresponding to the position ofthe amino acid residue in SEQ ID NO:2. For example, the inventionprovides polynucleotides encoding polypeptides comprising, oralternatively consisting of, an amino acid sequence selected from thegroup consisting of residues A-134 to Leu-285; A-134 to L-284; A-134 toK-283; A-134 to L-282; A-134 to A-281; A-134 to G-280; A-134 to F-279;A-134 to F-278; A-134 to T-277; A-134 to V-276; A-134 to D-275; A-134 toG-274; A-134 to D-273; A-134 to L-272; A-134 to S-271; A-134 to I-270;A-134 to Q-269; A-134 to A-268; A-134 to N-267; A-134 to E-266; A-134 toR-265; A-134 to P-264; A-134 to I-263; A-134 to A-262; A-134 to L-261;A-134 to Q-260; A-134 to L-259; A-134 to E-258; A-134 to D-257; A-134 toG-256; A-134 to E-255; A-134 to E-254; A-134 to L-253; A-134 to K-252;A-134 to A-251; A-134 to I-250; A-134 to G-249; A-134 to A-248; A-134 toS-247; A-134 to Y-246; A-134 to C-245; A-134 to S-244; A-134 to N-243;A-134 to N-242; A-134 to P-241; A-134 to L-240; A-134 to T-239; A-134 toE-238; A-134 to P-237; A-134 to M-236; A-134 to N-235; A-134 to Q-234;A-134 to I-233; A-134 to C-232; A-134 to R-231; A-134 to F-230; A-134 toL-229; A-134 to T-228; A-134 to V-227; A-134 to L-226; A-134 to S-225;A-134 to L-224; A-134 to E-223; A-134 to D-222; A-134 to G-221; A-134 toF-220; A-134 to V-219; A-134 to H-218; A-134 to V-217; A-134 to K-216;A-134 to K-215; A-134 to R-214; A-134 to Q-213; A-134 to I-212; A-134 toL-211; A-134 to H-210; A-134 to G-209; A-134 to M-208; A-134 to A-207;A-134 to Y-206; A-134 to T-205; A-134 to K-204; A-134 to D-203; A-134 toT-202; A-134 to Y-201; A-134 to L-200; A-134 to V-199; A-134 to Q-198;A-134 to G-197; A-134 to Y-196; A-134 to I-195; A-134 to F-194; A-134 toF-193; A-134 to Y-192; A-134 to G-191; A-134 to T-190; A-134 to E-189;A-134 to K-188; A-134 to V-187; A-134 to L-186; A-134 to I-185; A-134 toK-184; A-134 to N-183; A-134 to E-182; A-134 to K-181; A-134 to E-180;A-134 to E-179; A-134 to L-178; A-134 to A-177; A-134 to S-176; A-134 toG-175; A-134 to R-174; A-134 to K-173; A-134 to F-172; A-134 to S-171;A-134 to L-170; A-134 to L-169; A-134 to W-168; A-134 to P-167; A-134 toV-166; A-134 to F-165; A-134 to T-164; A-134 to Y-163; A-134 to S-162;A-134 to G-161; A-134 to K-160; A-134 to Q-159; A-134 to I-158; A-134 toT-157; A-134 to P-156; A-134 to T-155; A-134 to E-154; A-134 to S-153;A-134 to D-152; A-134 to A-151; A-134 to I-150; A-134 to L-149; A-134 toQ-148; A-134 to L-147; A-134 to C-146; A-134 to D-145; A-134 to Q-144;A-134 to T-143; A-134 to V-142; A-134 to T-141; and A-134 to E-140 ofSEQ ID NO:2. The present application is also directed to nucleic acidmolecules comprising, or alternatively, consisting of, a polynucleotidesequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99%identical to the polynucleotide sequence encoding the Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides described above. The presentinvention also encompasses the above polynucleotide sequences fused to aheterologous polynucleotide sequence. Polypeptides encoded by thesenucleic acids and/or polynucleotide sequences are also encompassed bythe invention, as are polypeptides comprising an amino acid sequence atleast 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to theamino acid sequence described above, and polynucleotides that encodesuch polypeptides.

Additional preferred polypeptide fragments of the invention comprise, oralternatively consist of, an amino acid sequence selected from the groupconsisting of residues: M-1 to C-15; D-2 to L-16; D-3 to K-17; S-4 toK-18; T-5 to R-19; E-6 to E-20; R-7 to E-21; E-8 to M-22; Q-9 to K-23;S-10 to L-24; R-11 to K-25; L-12 to E-26; T-13 to C-27; S-14 to V-28;C-15 to S-29; L-16 to I-30; K-17 to L-31; K-18 to P-32; R-19 to R-33;E-20 to K-34; E-21 to E-35; M-22 to S-36; K-23 to P-37; L-24 to S-38;K-25 to V-39; E-26 to R-40; C-27 to S-41; V-28 to S-42; S-29 to K-43;I-30 to D-44; L-31 to G-45; P-32 to K-46; R-33 to L-47; K-34 to L-48;E-35 to A-49; S-36 to A-50; P-37 to T-51; S-38 to L-52; V-39 to L-53;R-40 to L-54; S-41 to A-55; S-42 to L-56; K-43 to L-57; D-44 to S-58;G-45 to C-59; K-46 to C-60; L-47 to L-61; L-48 to T-62; A-49 to V-63;A-50 to V-64; T-51 to S-65; L-52 to F-66; L-53 to Y-67; L-54 to Q-68;A-55 to V-69; L-56 to A-70; L-57 to A-71; S-58 to L-72; C-59 to Q-73;C-60 to G-74; L-61 to D-75; T-62 to L-76; V-63 to A-77; V-64 to S-78;S-65 to L-79; F-66 to R-80; Y-67 to A-81; Q-68 to E-82; V-69 to L-83;A-70 to Q-84; A-71 to G-85; L-72 to H-86; Q-73 to H-87; G-74 to A-88;D-75 to E-89; L-76 to K-90; A-77 to L-91; S-78 to P-92; L-79 to A-93;R-80 to G-94; A-81 to A-95; E-82 to G-96; L-83 to A-97; Q-84 to P-98;G-85 to K-99; H-86 to A-100; H-87 to G-101; A-88 to L-102; E-89 toE-103; K-90 to E-104; L-91 to A-105; P-92 to P-106; A-93 to A-107; G-94to V-108; A-95 to T-109; G-96 to A-110; A-97 to G-111; P-98 to L-112;K-99 to K-113; A-100 to I-114; G-101 to F-115; L-102 to E-116; E-103 toP-117; E-104 to P-118; A-105 to A-119; P-106 to P-120; A-107 to G-121;V-108 to E-122; T-109 to G-123; A-110 to N-124; G-111 to S-125; L-112 toS-126; K-113 to Q-127; I-114 to N-128; F-115 to S-129; E-116 to R-130;P-117 to N-131; P-118 to K-132; A-119 to R-133; P-120 to A-134; G-121 toV-135; E-122 to Q-136; G-123 to G-137; N-124 to P-138; S-125 to E-139;S-126 to E-140; Q-127 to T-141; N-128 to V-142; S-129 to T-143; R-130 toQ-144; N-131 to D-145; K-132 to C-146; R-133 to L-147; A-134 to Q-148;V-135 to L-149; Q-136 to I-150; G-137 to A-151; P-138 to D-152; E-139 toS-153; E-140 to E-154; T-141 to T-155; V-142 to P-156; T-143 to T-157;Q-144 to I-158; D-145 to Q-159; C-146 to K-160; L-147 to G-161; Q-148 toS-162; L-149 to Y-163; I-150 to T-164; A-151 to F-165; D-152 to V-166;S-153 to P-167; E-154 to W-168; T-155 to L-169; P-156 to L-170; T-157 toS-171; I-158 to F-172; Q-159 to K-173; K-160 to R-174; G-161 to G-175;S-162 to S-176; Y-163 to A-177; T-164 to L-178; F-165 to E-179; V-166 toE-180; P-167 to K-181; W-168 to E-182; L-169 to N-183; L-170 to K-184;S-171 to I-185; F-172 to L-186; K-173 to V-187; R-174 to K-188; G-175 toE-189; S-176 to T-190; A-177 to G-191; L-178 to Y-192; E-179 to F-193;E-180 to F-194; K-181 to I-195; E-182 to Y-196; N-183 to G-197; K-184 toQ-198; I-185 to V-199; L-186 to L-200; V-187 to Y-201; K-188 to T-202;E-189 to D-203; T-190 to K-204; G-191 to T-205; Y-192 to Y-206; F-193 toA-207; F-194 to M-208; I-195 to G-209; Y-196 to H-210; G-197 to L-211;Q-198 to I-212; V-199 to Q-213; L-200 to R-214; Y-201 to K-215; T-202 toK-216; D-203 to V-217; K-204 to H-218; T-205 to V-219; Y-206 to F-220;A-207 to G-221; M-208 to D-222; G-209 to E-223; H-210 to L-224; L-211 toS-225; I-212 to L-226; Q-213 to V-227; R-214 to T-228; K-215 to L-229;K-216 to F-230; V-217 to R-231; H-218 to C-232; V-219 to I-233; F-220 toQ-234; G-221 to N-235; D-222 to M-236; E-223 to P-237; L-224 to E-238;S-225 to T-239; L-226 to L-240; V-227 to P-241; T-228 to N-242; L-229 toN-243; F-230 to S-244; R-231 to C-245; C-232 to Y-246; I-233 to S-247;Q-234 to A-248; N-235 to G-249; M-236 to I-250; P-237 to A-251; E-238 toK-252; T-239 to L-253; L-240 to E-254; P-241 to E-255; N-242 to G-256;N-243 to D-257; S-244 to E-258; C-245 to L-259; Y-246 to Q-260; S-247 toL-261; A-248 to A-262; G-249 to I-263; I-250 to P-264; A-251 to R-265;K-252 to E-266; L-253 to N-267; E-254 to A-268; E-255 to Q-269; G-256 toI-270; D-257 to S-271; E-258 to L-272; L-259 to D-273; Q-260 to G-274;L-261 to D-275; A-262 to V-276; I-263 to T-277; P-264 to F-278; R-265 toF-279; E-266 to G-280; N-267 to A-281; A-268 to L-282; Q-269 to K-283;I-270 to L-284; and S-271 to L-285 of SEQ ID NO:2. Preferably, thesepolypeptide fragments have one or more functional activities (e.g.,biological activity, antigenicity, and immunogenicity) ofNeutrokine-alpha and/or Neutrokine-alpha SV polypeptides of theinvention and may be used, for example, to generate or screen forantibodies, as described further below. The present invention is alsodirected to polypeptides comprising, or alternatively, consisting of, anamino acid sequence at least 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or99% identical to an amino acid sequence described above. The presentinvention also encompasses the above amino acid sequences fused to aheterologous amino acid sequence as described herein. Polynucleotidesencoding these polypeptides are also encompassed by the invention.

Additional preferred polypeptide fragments of the invention comprise, oralternatively consist of, an amino acid sequence selected from the groupconsisting of residues: M-1 to C-15; D-2 to L-16; D-3 to K-17; S-4 toK-18; T-5 to R-19; E-6 to E-20; R-7 to E-21; E-8 to M-22; Q-9 to K-23;S-10 to L-24; R-11 to K-25; L-12 to E-26; T-13 to C-27; S-14 to V-28;C-15 to S-29; L-16 to I-30; K-17 to L-31; K-18 to P-32; R-19 to R-33;E-20 to K-34; E-21 to E-35; M-22 to S-36; K-23 to P-37; L-24 to S-38;K-25 to V-39; E-26 to R-40; C-27 to S-41; V-28 to S-42; S-29 to K-43;I-30 to D-44; L-31 to G-45; P-32 to K-46; R-33 to L-47; K-34 to L-48;E-35 to A-49; S-36 to A-50; P-37 to T-51; S-38 to L-52; V-39 to L-53;R-40 to L-54; S-41 to A-55; S-42 to L-56; K-43 to L-57; D-44 to S-58;G-45 to C-59; K-46 to C-60; L-47 to L-61; L-48 to T-62; A-49 to V-63;A-50 to V-64; T-51 to S-65; L-52 to F-66; L-53 to Y-67; L-54 to Q-68;A-55 to V-69; L-56 to A-70; L-57 to A-71; S-58 to L-72; C-59 to Q-73;C-60 to G-74; L-61 to D-75; T-62 to L-76; V-63 to A-77; V-64 to S-78;S-65 to L-79; F-66 to R-80; Y-67 to A-81; Q-68 to E-82; V-69 to L-83;A-70 to Q-84; A-71 to G-85; L-72 to H-86; Q-73 to H-87; G-74 to A-88;D-75 to E-89; L-76 to K-90; A-77 to L-91; S-78 to P-92; L-79 to A-93;R-80 to G-94; A-81 to A-95; E-82 to G-96; L-83 to A-97; Q-84 to P-98;G-85 to K-99; H-86 to A-100; H-87 to G-101; A-88 to L-102; E-89 toE-103; K-90 to E-104; L-91 to A-105; P-92 to P-106; A-93 to A-107; G-94to V-108; A-95 to T-109; G-96 to A-110; A-97 to G-111; P-98 to L-112;K-99 to K-113; A-100 to I-114; G-101 to F-115; L-102 to E-116; E-103 toP-117; E-104 to P-118; A-105 to A-119; P-106 to P-120; A-107 to G-121;V-108 to E-122; T-109 to G-123; A-110 to N-124; G-111 to S-125; L-112 toS-126; K-113 to Q-127; I-114 to N-128; F-115 to S-129; E-116 to R-130;P-117 to N-131; P-118 to K-132; A-119 to R-133; P-120 to A-134; G-121 toV-135; E-122 to Q-136; G-123 to G-137; N-124 to P-138; S-125 to E-139;S-126 to E-140; Q-127 to T-141; N-128 to G-142; S-129 to S-143; R-130 toY-144; N-131 to T-145; K-132 to F-146; R-133 to V-147; A-134 to P-148;V-135 to W-149; Q-136 to L-150; G-137 to L-151; P-138 to S-152; E-139 toF-153; E-140 to K-154; T-141 to R-155; G-142 to G-156; S-143 to S-157;Y-144 to A-158; T-145 to L-159; F-146 to E-160; V-147 to E-161; P-148 toK-162; W-149 to E-163; L-150 to N-164; L-151 to K-165; S-152 to I-166;F-153 to L-167; K-154 to V-168; R-155 to K-169; G-156 to E-170; S-157 toT-171; A-158 to G-172; L-159 to Y-173; E-160 to F-174; E-161 to F-175;K-162 to I-176; E-163 to Y-177; N-164 to G-178; K-165 to Q-179; I-166 toV-180; L-167 to L-181; V-168 to Y-182; K-169 to T-183; E-170 to D-184;T-171 to K-185; G-172 to T-186; Y-173 to Y-187; F-174 to A-188; F-175 toM-189; I-176 to G-190; Y-177 to H-191; G-178 to L-192; Q-179 to I-193;V-180 to Q-194; L-181 to R-195; Y-182 to K-196; T-183 to K-197; D-184 toV-198; K-185 to H-199; T-186 to V-200; Y-187 to F-201; A-188 to G-202;M-189 to D-203; G-190 to E-204; H-191 to L-205; L-192 to S-206; I-193 toL-207; Q-194 to V-208; R-195 to T-209; K-196 to L-210; K-197 to F-211;V-198 to R-212; H-199 to C-213; V-200 to I-214; F-201 to Q-215; G-202 toN-216; D-203 to M-217; E-204 to P-218; L-205 to E-219; S-206 to T-220;L-207 to L-221; V-208 to P-222; T-209 to N-223; L-210 to N-224; F-211 toS-225; R-212 to C-226; C-213 to Y-227; I-214 to S-228; Q-215 to A-229;N-216 to G-230; M-217 to I-231; P-218 to A-232; E-219 to K-233; T-220 toL-234; L-221 to E-235; P-222 to E-236; N-223 to G-237; N-224 to D-238;S-225 to E-239; C-226 to L-240; Y-227 to Q-241; S-228 to L-242; A-229 toA-243; G-230 to I-244; I-231 to P-245; A-232 to R-246; K-233 to E-247;L-234 to N-248; E-235 to A-249; E-236 to Q-250; G-237 to I-251; D-238 toS-252; E-239 to L-253; L-240 to D-254; Q-241 to G-255; L-242 to D-256;A-243 to V-257; I-244 to T-258; P-245 to F-259; R-246 to F-260; E-247 toG-261; N-248 to A-262; A-249 to L-263; Q-250 to K-264; I-251 to L-265;and S-252 to L-266 of SEQ ID NO:19. Preferably, these polypeptidefragments have one or more functional activities (e.g., biologicalactivity, antigenicity, and immunogenicity) of Neutrokine-alpha and/orNeutrokine-alpha SV polypeptides of the invention and may be used, forexample, to generate or screen for antibodies, as described furtherbelow. The present invention is also directed to polypeptidescomprising, or alternatively, consisting of, an amino acid sequence atleast 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to anamino acid sequence described above. The present invention alsoencompasses the above amino acid sequences fused to a heterologous aminoacid sequence as described herein. Polynucleotides encoding thesepolypeptides are also encompassed by the invention.

Additional preferred polypeptide fragments of the invention comprise, oralternatively consist of, an amino acid sequence selected from the groupconsisting of residues: M-1 to F-15; D-2 to C-16; E-3 to S-17; S-4 toE-18; A-5 to K-19; K-6 to G-20; T-7 to E-21; L-8 to D-22; P-9 to M-23;P-10 to K-24; P-11 to V-25; C-12 to G-26; L-13 to Y-27; C-14 to D-28;F-15 to P-29; C-16 to I-30; S-17 to T-31; E-18 to P-32; K-19 to Q-33;G-20 to K-34; E-21 to E-35; D-22 to E-36; M-23 to G-37; K-24 to A-38;V-25 to W-39; G-26 to F-40; Y-27 to G-41; D-28 to I-42; P-29 to C-43;I-30 to R-44; T-31 to D-45; P-32 to G-46; Q-33 to R-47; K-34 to L-48;E-35 to L-49; E-36 to A-50; G-37 to A-51; A-38 to T-52; W-39 to L-53;F-40 to L-54; G-41 to L-55; I-42 to A-56; C-43 to L-57; R-44 to L-58;D-45 to S-59; G-46 to S-60; R-47 to S-61; L-48 to F-62; L-49 to T-63;A-50 to A-64; A-51 to M-65; T-52 to S-66; L-53 to L-67; L-54 to Y-68;L-55 to Q-69; A-56 to L-70; L-57 to A-71; L-58 to A-72; S-59 to L-73;S-60 to Q-74; S-61 to A-75; F-62 to D-76; T-63 to L-77; A-64 to M-78;M-65 to N-79; S-66 to L-80; L-67 to R-81; Y-68 to M-82; Q-69 to E-83;L-70 to L-84; A-71 to Q-85; A-72 to S-86; L-73 to Y-87; Q-74 to R-88;A-75 to G-89; D-76 to S-90; L-77 to A-91; M-78 to T-92; N-79 to P-93;L-80 to A-94; R-81 to A-95; M-82 to A-96; E-83 to G-97; L-84 to A-98;Q-85 to P-99; S-86 to E-100; Y-87 to L-101; R-88 to T-102; G-89 toA-103; S-90 to G-104; A-91 to V-105; T-92 to K-106; P-93 to L-107; A-94to L-108; A-95 to T-109; A-96 to P-110; G-97 to A-111; A-98 to A-112;P-99 to P-113; E-100 to R-114; L-101 to P-115; T-102 to H-116; A-103 toN-117; G-104 to S-118; V-105 to S-119; K-106 to R-120; L-107 to G-121;L-108 to H-122; T-109 to R-123; P-110 to N-124; A-111 to R-125; A-112 toR-126; P-113 to A-127; R-114 to F-128; P-115 to Q-129; H-116 to G-130;N-117 to P-131; S-118 to E-132; S-119 to E-133; R-120 to T-134; G-121 toE-135; H-122 to Q-136; R-123 to D-137; N-124 to V-138; R-125 to D-139;R-126 to L-140; A-127 to S-141; F-128 to A-142; Q-129 to P-143; G-130 toP-144; P-131 to A-145; E-132 to P-146; E-133 to C-147; T-134 to L-148;E-135 to P-149; Q-136 to G-150; D-137 to C-151; V-138 to R-152; D-139 toH-153; L-140 to S-154; S-141 to Q-155; A-142 to H-156; P-143 to D-157;P-144 to D-158; A-145 to N-159; P-146 to G-160; C-147 to M-161; L-148 toN-162; P-149 to L-163; G-150 to R-164; C-151 to N-165; R-152 to I-166;H-153 to I-167; S-154 to Q-168; Q-155 to D-169; H-156 to C-170; D-157 toL-171; D-158 to Q-172; N-159 to L-173; G-160 to I-174; M-161 to A-175;N-162 to D-176; L-163 to S-177; R-164 to D-178; N-165 to T-179; I-166 toP-180; I-167 to A-181; Q-168 to L-182; D-169 to E-183; C-170 to E-184;L-171 to K-185; Q-172 to E-186; L-173 to N-187; I-174 to K-188; A-175 toI-189; D-176 to V-190; S-177 to V-191; D-178 to R-192; T-179 to Q-193;P-180 to T-194; A-181 to G-195; L-182 to Y-196; E-183 to F-197; E-184 toF-198; K-185 to I-199; E-186 to Y-200; N-187 to S-201; K-188 to Q-202;I-189 to V-203; V-190 to L-204; V-191 to Y-205; R-192 to T-206; Q-193 toD-207; T-194 to P-208; G-195 to I-209; Y-196 to F-210; F-197 to A-211;F-198 to M-212; I-199 to G-213; Y-200 to H-214; S-201 to V-215; Q-202 toI-216; V-203 to Q-217; L-204 to R-218; Y-205 to K-219; T-206 to K-220;D-207 to V-221; P-208 to H-222; I-209 to V-223; F-210 to F-224; A-211 toG-225; M-212 to D-226; G-213 to E-227; H-214 to L-228; V-215 to S-229;I-216 to L-230; Q-217 to V-231; R-218 to T-232; K-219 to L-233; K-220 toF-234; V-221 to R-235; H-222 to C-236; V-223 to I-237; F-224 to Q-238;G-225 to N-239; D-226 to M-240; E-227 to P-241; L-228 to K-242; S-229 toT-243; L-230 to L-244; V-231 to P-245; T-232 to N-246; L-233 to N-247;F-234 to S-248; R-235 to C-249; C-236 to Y-250; I-237 to S-251; Q-238 toA-252; N-239 to G-253; M-240 to I-254; P-241 to A-255; K-242 to R-256;T-243 to L-257; L-244 to E-258; P-245 to E-259; N-246 to G-260; N-247 toD-261; S-248 to E-262; C-249 to I-263; Y-250 to Q-264; S-251 to L-265;A-252 to A-266; G-253 to I-267; I-254 to P-268; A-255 to R-269; R-256 toE-270; L-257 to N-271; E-258 to A-272; E-259 to Q-273; G-260 to I-274;D-261 to S-275; E-262 to R-276; I-263 to N-277; Q-264 to G-278; L-265 toD-279; A-266 to D-280; I-267 to T-281; P-268 to F-282; R-269 to F-283;E-270 to G-284; N-271 to A-285; A-272 to L-286; Q-273 to K-287; I-274 toL-288; and S-275 to L-289 of SEQ ID NO:38. Preferably, these polypeptidefragments have one or more functional activities (e.g., biologicalactivity, antigenicity, and immunogenicity) of Neutrokine-alpha and/orNeutrokine-alpha SV polypeptides of the invention and may be used, forexample, to generate or screen for antibodies, as described furtherbelow. The present invention is also directed to polypeptidescomprising, or alternatively, consisting of, an amino acid sequence atleast 80%, 85%, 90%, 92%, 95%, 96%, 97%, 98% or 99% identical to anamino acid sequence described above. The present invention alsoencompasses the above amino acid sequences fused to a heterologous aminoacid sequence as described herein. Polynucleotides encoding thesepolypeptides are also encompassed by the invention.

It will be recognized by one of ordinary skill in the art that someamino acid sequences of the Neutrokine-alpha and Neutrokine-alphaSVpolypeptides can be varied without significant effect of the structureor function of the polypeptide. If such differences in sequence arecontemplated, it should be remembered that there will be critical areason the polypeptide which determine activity.

Thus, the invention further includes variations of the Neutrokine-alphapolypeptide which show Neutrokine-alpha polypeptide functional activity(e.g., biological activity) or which include regions of Neutrokine-alphapolypeptide such as the polypeptide fragments described herein. Theinvention also includes variations of the Neutrokine-alphaSV polypeptidewhich show Neutrokine-alphaSV polypeptide functional activity (e.g.,biological activity) or which include regions of Neutrokine-alphaSVpolypeptide such as the polypeptide fragments described herein. Suchmutants include deletions, insertions, inversions, repeats, and typesubstitutions selected according to general rules known in the art so ashave little effect on activity. For example, guidance concerning how tomake phenotypically silent amino acid substitutions is provided inBowie, J. U. et al., “Deciphering the Message in Protein Sequences:Tolerance to Amino Acid Substitutions,” Science 247:1306-1310 (1990),wherein the authors indicate that there are two main approaches forstudying the tolerance of an amino acid sequence to change. The firstmethod relies on the process of evolution, in which mutations are eitheraccepted or rejected by natural selection. The second approach usesgenetic engineering to introduce amino acid changes at specificpositions of a cloned gene and selections or screens to identifysequences that maintain functionality.

As the authors state, these studies have revealed that proteins aresurprisingly tolerant of amino acid substitutions. The authors furtherindicate which amino acid changes are likely to be permissive at acertain position of the protein. For example, most buried amino acidresidues require nonpolar side chains, whereas few features of surfaceside chains are generally conserved. Other such phenotypically silentsubstitutions are described in Bowie, J. U. et al., supra, and thereferences cited therein. Typically seen as conservative substitutionsare the replacements, one for another, among the aliphatic amino acidsAla, Val, Leu and Ile; interchange of the hydroxyl residues Ser and Thr,exchange of the acidic residues Asp and Glu, substitution between theamide residues Asn and Gln, exchange of the basic residues Lys and Argand replacements among the aromatic residues Phe, Tyr.

Thus, the fragment, derivative or analog of the polypeptide of FIGS. 1Aand 1B (SEQ ID NO:2), or that encoded by the deposited cDNA plasmid, maybe (i) one in which one or more of the amino acid residues aresubstituted with a conserved or non-conserved amino acid residue(preferably a conserved amino acid residue) and such substituted aminoacid residue may or may not be one encoded by the genetic code, or (ii)one in which one or more of the amino acid residues includes asubstituent group, or (iii) one in which the extracellular domain of thepolypeptide is fused with another compound, such as a compound toincrease the half-life of the polypeptide (for example, polyethyleneglycol), or (iv) one in which the additional amino acids are fused tothe extracellular domain of the polypeptide, such as an IgG Fc fusionregion peptide or leader or secretory sequence or a sequence which isemployed for purification of the extracellular domain of the polypeptideor a proprotein sequence. Such fragments, derivatives and analogs aredeemed to be within the scope of those skilled in the art from theteachings herein

Furthermore, the fragment, derivative or analog of the polypeptide ofFIGS. 5A and 5B (SEQ ID NO:19), or that encoded by the deposited cDNAplasmid, may be (i) one in which one or more of the amino acid residuesare substituted with a conserved or non-conserved amino acid residue(preferably a conserved amino acid residue) and such substituted aminoacid residue may or may not be one encoded by the genetic code, or (ii)one in which one or more of the amino acid residues includes asubstituent group, or (iii) one in which the extracellular domain of thepolypeptide is fused with another compound, such as a compound toincrease the half-life of the polypeptide (for example, polyethyleneglycol), or (iv) one in which the additional amino acids are fused tothe extracellular domain of the polypeptide, such as, a solublebiologically active fragment of another TNF ligand family member (e.g.,CD40 Ligand), an IgG Fc fusion region peptide or leader or secretorysequence or a sequence which is employed for purification of theextracellular domain of the polypeptide or a proprotein sequence. Suchfragments, derivatives and analogs are deemed to be within the scope ofthose skilled in the art from the teachings herein

Thus, the Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides of thepresent invention may include one or more amino acid substitutions,deletions or additions, either from natural mutations or humanmanipulation. As indicated, changes are preferably of a minor nature,such as conservative amino acid substitutions that do not significantlyaffect the folding or activity of the protein (see Table II).

TABLE II Conservative Amino Acid Substitutions. Aromatic PhenylalanineTryptophan Tyrosine Hydrophobic Leucine Isoleucine Valine PolarGlutamine Asparagine Basic Arginine Lysine Histidine Acidic AsparticAcid Glutamic Acid Small Alanine Serine Threonine Methionine Glycine

In one embodiment of the invention, polypeptide comprises, oralternatively consists of, the amino acid sequence of a Neutrokine-alphaor Neutrokine-alphaSV polypeptide having an amino acid sequence whichcontains at least one conservative amino acid substitution, but not morethan 50 conservative amino acid substitutions, even more preferably, notmore than 40 conservative amino acid substitutions, still morepreferably, not more than 30 conservative amino acid substitutions, andstill even more preferably, not more than 20 conservative amino acidsubstitutions. Of course, in order of ever-increasing preference, it ishighly preferable for a peptide or polypeptide to have an amino acidsequence which comprises the amino acid sequence of a Neutrokine-alphapolypeptide, which contains at least one, but not more than 10, 9, 8, 7,6, 5, 4, 3, 2 or 1 conservative amino acid substitutions.

For example, site directed changes at the amino acid level ofNeutrokine-alpha can be made by replacing a particular amino acid with aconservative substitution. Preferred conservative substitution mutationsof the Neutrokine-alpha amino acid sequence provided in SEQ ID NO:2include: M1 replaced with A, G, I, L, S, T, or V; D2 replaced with E; D3replaced with E; S4 replaced with A, G, I, L, T, M, or V; T5 replacedwith A, G, I, L, S, M, or V; E6 replaced with D; R7 replaced with H, orK; E8 replaced with D; Q9 replaced with N; S10 replaced with A, G, I, L,T, M, or V; R11 replaced with H, or K; L12 replaced with A, G, I, S, T,M, or V; T13 replaced with A, G, I, L, S, M, or V; S14 replaced with A,G, I, L, T, M, or V; L16 replaced with A, G, I, S, T, M, or V; K17replaced with H, or R; K18 replaced with H, or R; R19 replaced with H,or K; E20 replaced with D; E21 replaced with D; M22 replaced with A, G,I, L, S, T, or V; K23 replaced with H, or R; L24 replaced with A, G, I,S, T, M, or V; K25 replaced with H, or R; E26 replaced with D; V28replaced with A, G, I, L, S, T, or M; S29 replaced with A, G, I, L, T,M, or V; I30 replaced with A, G, L, S, T, M, or V; L31 replaced with A,G, I, S, T, M, or V; R33 replaced with H, or K; K34 replaced with H, orR; E35 replaced with D; S36 replaced with A, G, I, L, T, M, or V; S38replaced with A, G, I, L, T, M, or V; V39 replaced with A, G, I, L, S,T, or M; R40 replaced with H, or K; S41 replaced with A, G, I, L, T, M,or V; S42 replaced with A, G, I, L, T, M, or V; K43 replaced with H, orR; D44 replaced with E; G45 replaced with A, I, L, S, T, M, or V; K46replaced with H, or R; L47 replaced with A, G, I, S, T, M, or V; L48replaced with A, G, I, S, T, M, or V; A49 replaced with G, I, L, S, T,M, or V; A50 replaced with G, I, L, S, T, M, or V; T51 replaced with A,G, I, L, S, M, or V; L52 replaced with A, G, I, S, T, M, or V; L53replaced with A, G, I, S, T, M, or V; L54 replaced with A, G, I, S, T,M, or V; A55 replaced with G, I, L, S, T, M, or V; L56 replaced with A,G, I, S, T, M, or V; L57 replaced with A, G, I, S, T, M, or V; S58replaced with A, G, I, L, T, M, or V; L61 replaced with A, G, I, S, T,M, or V; T62 replaced with A, G, I, L, S, M, or V; V63 replaced with A,G, I, L, S, T, or M; V64 replaced with A, G, I, L, S, T, or M; S65replaced with A, G, I, L, T, M, or V; F66 replaced with W, or Y; Y67replaced with F, or W; Q68 replaced with N; V69 replaced with A, G, I,L, S, T, or M; A70 replaced with G, I, L, S, T, M, or V; A71 replacedwith G, I, L, S, T, M, or V; L72 replaced with A, G, I, S, T, M, or V;Q73 replaced with N; G74 replaced with A, I, L, S, T, M, or V; D75replaced with E; L76 replaced with A, G, I, S, T, M, or V; A77 replacedwith G, I, L, S, T, M, or V; S78 replaced with A, G, I, L, T, M, or V;L79 replaced with A, G, I, S, T, M, or V; R80 replaced with H, or K; A81replaced with G, I, L, S, T, M, or V; E82 replaced with D; L83 replacedwith A, G, I, S, T, M, or V; Q84 replaced with N; G85 replaced with A,I, L, S, T, M, or V; H86 replaced with K, or R; H87 replaced with K, orR; A88 replaced with G, I, L, S, T, M, or V; E89 replaced with D; K90replaced with H, or R; L91 replaced with A, G, I, S, T, M, or V; A93replaced with G, I, L, S, T, M, or V; G94 replaced with A, I, L, S, T,M, or V; A95 replaced with G, I, L, S, T, M, or V; G96 replaced with A,I, L, S, T, M, or V; A97 replaced with G, I, L, S, T, M, or V; K99replaced with H, or R; A100 replaced with G, I, L, S, T, M, or V; G101replaced with A, I, L, S, T, M, or V; L102 replaced with A, G, I, S, T,M, or V; E103 replaced with D; E104 replaced with D; A105 replaced withG, I, L, S, T, M, or V; A107 replaced with G, I, L, S, T, M, or V; V108replaced with A, G, I, L, S, T, or M; T109 replaced with A, G, I, L, S,M, or V; A110 replaced with G, I, L, S, T, M, or V; G111 replaced withA, I, L, S, T, M, or V; L112 replaced with A, G, I, S, T, M, or V; K113replaced with H, or R; I114 replaced with A, G, L, S, T, M, or V; F115replaced with W, or Y; E116 replaced with D; A119 replaced with G, I, L,S, T, M, or V; G121 replaced with A, I, L, S, T, M, or V; E122 replacedwith D; G123 replaced with A, I, L, S, T, M, or V; N124 replaced with Q;S125 replaced with A, G, I, L, T, M, or V; S126 replaced with A, G, I,L, T, M, or V; Q127 replaced with N; N128 replaced with Q; S129 replacedwith A, G, I, L, T, M, or V; R130 replaced with H, or K; N131 replacedwith Q; K132 replaced with H, or R; R133 replaced with H, or K; A134replaced with G, I, L, S, T, M, or V; V135 replaced with A, G, I, L, S,T, or M; Q136 replaced with N; G137 replaced with A, I, L, S, T, M, orV; E139 replaced with D; E140 replaced with D; T141 replaced with A, G,I, L, S, M, or V; V142 replaced with A, G, I, L, S, T, or M; T143replaced with A, G, I, L, S, M, or V; Q144 replaced with N; D145replaced with E; L147 replaced with A, G, I, S, T, M, or V; Q148replaced with N; L149 replaced with A, G, I, S, T, M, or V; I150replaced with A, G, L, S, T, M, or V; A151 replaced with G, I, L, S, T,M, or V; D152 replaced with E; S153 replaced with A, G, I, L, T, M, orV; E154 replaced with D; T155 replaced with A, G, I, L, S, M, or V; T157replaced with A, G, I, L, S, M, or V; I158 replaced with A, G, L, S, T,M, or V; Q159 replaced with N; K160 replaced with H, or R; G161 replacedwith A, I, L, S, T, M, or V; S162 replaced with A, G, I, L, T, M, or V;Y163 replaced with F, or W; T164 replaced with A, G, I, L, S, M, or V;F165 replaced with W, or Y; V166 replaced with A, G, I, L, S, T, or M;W168 replaced with F, or Y; L169 replaced with A, G, I, S, T, M, or V;L170 replaced with A, G, I, S, T, M, or V; S171 replaced with A, G, I,L, T, M, or V; F172 replaced with W, or Y; K173 replaced with H, or R;R174 replaced with H, or K; G175 replaced with A, I, L, S, T, M, or V;S176 replaced with A, G, I, L, T, M, or V; A177 replaced with G, I, L,S, T, M, or V; L178 replaced with A, G, I, S, T, M, or V; E179 replacedwith D; E180 replaced with D; K181 replaced with H, or R; E182 replacedwith D; N183 replaced with Q; K184 replaced with H, or R; I185 replacedwith A, G, L, S, T, M, or V; L186 replaced with A, G, I, S, T, M, or V;V187 replaced with A, G, I, L, S, T, or M; K188 replaced with H, or R;E189 replaced with D; T190 replaced with A, G, I, L, S, M, or V; G191replaced with A, I, L, S, T, M, or V; Y192 replaced with F, or W; F193replaced with W, or Y; F194 replaced with W, or Y; I195 replaced with A,G, L, S, T, M, or V; Y196 replaced with F, or W; G197 replaced with A,I, L, S, T, M, or V; Q198 replaced with N; V199 replaced with A, G, I,L, S, T, or M; L200 replaced with A, G, I, S, T, M, or V; Y201 replacedwith F, or W; T202 replaced with A, G, I, L, S, M, or V; D203 replacedwith E; K204 replaced with H, or R; T205 replaced with A, G, I, L, S, M,or V; Y206 replaced with F, or W; A207 replaced with G, I, L, S, T, M,or V; M208 replaced with A, G, I, L, S, T, or V; G209 replaced with A,I, L, S, T, M, or V; H210 replaced with K, or R; L211 replaced with A,G, I, S, T, M, or V; I212 replaced with A, G, L, S, T, M, or V; Q213replaced with N; R214 replaced with H, or K; K215 replaced with H, or R;K216 replaced with H, or R; V217 replaced with A, G, I, L, S, T, or M;H218 replaced with K, or R; V219 replaced with A, G, I, L, S, T, or M;F220 replaced with W, or Y; G221 replaced with A, I, L, S, T, M, or V;D222 replaced with E; E223 replaced with D; L224 replaced with A, G, I,S, T, M, or V; S225 replaced with A, G, I, L, T, M, or V; L226 replacedwith A, G, I, S, T, M, or V; V227 replaced with A, G, I, L, S, T, or M;T228 replaced with A, G, I, L, S, M, or V; L229 replaced with A, G, I,S, T, M, or V; F230 replaced with W, or Y; R231 replaced with H, or K;I233 replaced with A, G, L, S, T, M, or V; Q234 replaced with N; N235replaced with Q; M236 replaced with A, G, I, L, S, T, or V; E238replaced with D; T239 replaced with A, G, I, L, S, M, or V; L240replaced with A, G, I, S, T, M, or V; N242 replaced with Q; N243replaced with Q; S244 replaced with A, G, I, L, T, M, or V; Y246replaced with F, or W; S247 replaced with A, G, I, L, T, M, or V; A248replaced with G, I, L, S, T, M, or V; G249 replaced with A, I, L, S, T,M, or V; I250 replaced with A, G, L, S, T, M, or V; A251 replaced withG, I, L, S, T, M, or V; K252 replaced with H, or R; L253 replaced withA, G, I, S, T, M, or V; E254 replaced with D; E255 replaced with D; G256replaced with A, I, L, S, T, M, or V; D257 replaced with E; E258replaced with D; L259 replaced with A, G, I, S, T, M, or V; Q260replaced with N; L261 replaced with A, G, I, S, T, M, or V; A262replaced with G, I, L, S, T, M, or V; I263 replaced with A, G, L, S, T,M, or V; R265 replaced with H, or K; E266 replaced with D; N267 replacedwith Q; A268 replaced with G, I, L, S, T, M, or V; Q269 replaced with N;I270 replaced with A, G, L, S, T, M, or V; S271 replaced with A, G, I,L, T, M, or V; L272 replaced with A, G, I, S, T, M, or V; D273 replacedwith E; G274 replaced with A, I, L, S, T, M, or V; D275 replaced with E;V276 replaced with A, G, I, L, S, T, or M; T277 replaced with A, G, I,L, S, M, or V; F278 replaced with W, or Y; F279 replaced with W, or Y;G280 replaced with A, I, L, S, T, M, or V; A281 replaced with G, I, L,S, T, M, or V; L282 replaced with A, G, I, S, T, M, or V; K283 replacedwith H, or R; L284 replaced with A, G, I, S, T, M, or V; and/or L285replaced with A, G, I, S, T, M, or V. Polynucleotides encoding thesepolypeptides are also encompassed by the invention. The resultingNeutrokine-alpha proteins of the invention may be routinely screened forNeutrokine-alpha and/or Neutrokine-alphaSV functional activity and/orphysical properties (such as, for example, enhanced or reduced stabilityand/or solubility). Preferably, the resulting proteins of the inventionhave an increased and/or a decreased Neutrokine-alpha and/orNeutrokine-alphaSV functional activity. More preferably, the resultingNeutrokine-alpha and/or Neutrokine-alphaSV proteins of the inventionhave more than one increased and/or decreased Neutrokine-alpha and/orNeutrokine-alpha SV functional activity and/or physical property.

In another embodiment, site directed changes at the amino acid level ofNeutrokine-alphaSV can be made by replacing a particular amino acid witha conservative substitution. Preferred conservative substitutionmutations of the Neutrokine-alphaSV amino acid sequence provided in SEQID NO:19 include: M1 replaced with A, G, I, L, S, T, or V; D2 replacedwith E; D3 replaced with E; S4 replaced with A, G, I, L, T, M, or V; T5replaced with A, G, I, L, S, M, or V; E6 replaced with D; R7 replacedwith H, or K; E8 replaced with D; Q9 replaced with N; S10 replaced withA, G, I, L, T, M, or V; R11 replaced with H, or K; L12 replaced with A,G, I, S, T, M, or V; T13 replaced with A, G, I, L, S, M, or V; S14replaced with A, G, I, L, T, M, or V; L16 replaced with A, G, I, S, T,M, or V; K17 replaced with H, or R; K18 replaced with H, or R; R19replaced with H, or K; E20 replaced with D; E21 replaced with D; M22replaced with A, G, I, L, S, T, or V; K23 replaced with H, or R; L24replaced with A, G, I, S, T, M, or V; K25 replaced with H, or R; E26replaced with D; V28 replaced with A, G, I, L, S, T, or M; S29 replacedwith A, G, I, L, T, M, or V; I30 replaced with A, G, L, S, T, M, or V;L31 replaced with A, G, I, S, T, M, or V; R33 replaced with H, or K; K34replaced with H, or R; E35 replaced with D; S36 replaced with A, G, I,L, T, M, or V; S38 replaced with A, G, I, L, T, M, or V; V39 replacedwith A, G, I, L, S, T, or M; R40 replaced with H, or K; S41 replacedwith A, G, I, L, T, M, or V; S42 replaced with A, G, I, L, T, M, or V;K43 replaced with H, or R; D44 replaced with E; G45 replaced with A, I,L, S, T, M, or V; K46 replaced with H, or R; L47 replaced with A, G, I,S, T, M, or V; L48 replaced with A, G, I, S, T, M, or V; A49 replacedwith G, I, L, S, T, M, or V; A50 replaced with G, I, L, S, T, M, or V;T51 replaced with A, G, I, L, S, M, or V; L52 replaced with A, G, I, S,T, M, or V; L53 replaced with A, G, I, S, T, M, or V; L54 replaced withA, G, I, S, T, M, or V; A55 replaced with G, I, L, S, T, M, or V; L56replaced with A, G, I, S, T, M, or V; L57 replaced with A, G, I, S, T,M, or V; S58 replaced with A, G, I, L, T, M, or V; L61 replaced with A,G, I, S, T, M, or V; T62 replaced with A, G, I, L, S, M, or V; V63replaced with A, G, I, L, S, T, or M; V64 replaced with A, G, I, L, S,T, or M; S65 replaced with A, G, I, L, T, M, or V; F66 replaced with W,or Y; Y67 replaced with F, or W; Q68 replaced with N; V69 replaced withA, G, I, L, S, T, or M; A70 replaced with G, I, L, S, T, M, or V; A71replaced with G, I, L, S, T, M, or V; L72 replaced with A, G, I, S, T,M, or V; Q73 replaced with N; G74 replaced with A, I, L, S, T, M, or V;D75 replaced with E; L76 replaced with A, G, I, S, T, M, or V; A77replaced with G, I, L, S, T, M, or V; S78 replaced with A, G, I, L, T,M, or V; L79 replaced with A, G, I, S, T, M, or V; R80 replaced with H,or K; A81 replaced with G, I, L, S, T, M, or V; E82 replaced with D; L83replaced with A, G, I, S, T, M, or V; Q84 replaced with N; G85 replacedwith A, I, L, S, T, M, or V; H86 replaced with K, or R; H87 replacedwith K, or R; A88 replaced with G, I, L, S, T, M, or V; E89 replacedwith D; K90 replaced with H, or R; L91 replaced with A, G, I, S, T, M,or V; A93 replaced with G, I, L, S, T, M, or V; G94 replaced with A, I,L, S, T, M, or V; A95 replaced with G, I, L, S, T, M, or V; G96 replacedwith A, I, L, S, T, M, or V; A97 replaced with G, I, L, S, T, M, or V;K99 replaced with H, or R; A100 replaced with G, I, L, S, T, M, or V;G101 replaced with A, I, L, S, T, M, or V; L102 replaced with A, G, I,S, T, M, or V; E103 replaced with D; E104 replaced with D; A105 replacedwith G, I, L, S, T, M, or V; A107 replaced with G, I, L, S, T, M, or V;V108 replaced with A, G, I, L, S, T, or M; T109 replaced with A, G, I,L, S, M, or V; A110 replaced with G, I, L, S, T, M, or V; G111 replacedwith A, I, L, S, T, M, or V; L112 replaced with A, G, I, S, T, M, or V;K113 replaced with H, or R; I114 replaced with A, G, L, S, T, M, or V;F115 replaced with W, or Y; E116 replaced with D; A119 replaced with G,I, L, S, T, M, or V; G121 replaced with A, I, L, S, T, M, or V; E122replaced with D; G123 replaced with A, I, L, S, T, M, or V; N124replaced with Q; S125 replaced with A, G, I, L, T, M, or V; S126replaced with A, G, I, L, T, M, or V; Q127 replaced with N; N128replaced with Q; S129 replaced with A, G, I, L, T, M, or V; R130replaced with H, or K; N131 replaced with Q; K132 replaced with H, or R;R133 replaced with H, or K; A134 replaced with G, I, L, S, T, M, or V;V135 replaced with A, G, I, L, S, T, or M; Q136 replaced with N; G137replaced with A, I, L, S, T, M, or V; E139 replaced with D; E140replaced with D; T141 replaced with A, G, I, L, S, M, or V; G142replaced with A, I, L, S, T, M, or V; S143 replaced with A, G, I, L, T,M, or V; Y144 replaced with F, or W; T145 replaced with A, G, I, L, S,M, or V; F146 replaced with W, or Y; V147 replaced with A, G, I, L, S,T, or M; W149 replaced with F, or Y; L150 replaced with A, G, I, S, T,M, or V; L151 replaced with A, G, I, S, T, M, or V; S152 replaced withA, G, I, L, T, M, or V; F153 replaced with W, or Y; K154 replaced withH, or R; R155 replaced with H, or K; G156 replaced with A, I, L, S, T,M, or V; S157 replaced with A, G, I, L, T, M, or V; A158 replaced withG, I, L, S, T, M, or V; L159 replaced with A, G, I, S, T, M, or V; E160replaced with D; E161 replaced with D; K162 replaced with H, or R; E163replaced with D; N164 replaced with Q; K165 replaced with H, or R; I166replaced with A, G, L, S, T, M, or V; L167 replaced with A, G, I, S, T,M, or V; V168 replaced with A, G, I, L, S, T, or M; K169 replaced withH, or R; E170 replaced with D; T171 replaced with A, G, I, L, S, M, orV; G172 replaced with A, I, L, S, T, M, or V; Y173 replaced with F, orW; F174 replaced with W, or Y; F175 replaced with W, or Y; I176 replacedwith A, G, L, S, T, M, or V; Y177 replaced with F, or W; G178 replacedwith A, I, L, S, T, M, or V; Q179 replaced with N; V180 replaced with A,G, I, L, S, T, or M; L181 replaced with A, G, I, S, T, M, or V; Y182replaced with F, or W; T183 replaced with A, G, I, L, S, M, or V; D184replaced with E; K185 replaced with H, or R; T186 replaced with A, G, I,L, S, M, or V; Y187 replaced with F, or W; A188 replaced with G, I, L,S, T, M, or V; M189 replaced with A, G, I, L, S, T, or V; G190 replacedwith A, I, L, S, T, M, or V; H191 replaced with K, or R; L192 replacedwith A, G, I, S, T, M, or V; I193 replaced with A, G, L, S, T, M, or V;Q194 replaced with N; R195 replaced with H, or K; K196 replaced with H,or R; K197 replaced with H, or R; V198 replaced with A, G, I, L, S, T,or M; H199 replaced with K, or R; V200 replaced with A, G, I, L, S, T,or M; F201 replaced with W, or Y; G202 replaced with A, I, L, S, T, M,or V; D203 replaced with E; E204 replaced with D; L205 replaced with A,G, I, S, T, M, or V; S206 replaced with A, G, I, L, T, M, or V; L207replaced with A, G, I, S, T, M, or V; V208 replaced with A, G, I, L, S,T, or M; T209 replaced with A, G, I, L, S, M, or V; L210 replaced withA, G, I, S, T, M, or V; F211 replaced with W, or Y; R212 replaced withH, or K; I214 replaced with A, G, L, S, T, M, or V; Q215 replaced withN; N216 replaced with Q; M217 replaced with A, G, I, L, S, T, or V; E219replaced with D; T220 replaced with A, G, I, L, S, M, or V; L221replaced with A, G, I, S, T, M, or V; N223 replaced with Q; N224replaced with Q; S225 replaced with A, G, I, L, T, M, or V; Y227replaced with F, or W; S228 replaced with A, G, I, L, T, M, or V; A229replaced with G, I, L, S, T, M, or V; G230 replaced with A, I, L, S, T,M, or V; I231 replaced with A, G, L, S, T, M, or V; A232 replaced withG, I, L, S, T, M, or V; K233 replaced with H, or R; L234 replaced withA, G, I, S, T, M, or V; E235 replaced with D; E236 replaced with D; G237replaced with A, I, L, S, T, M, or V; D238 replaced with E; E239replaced with D; L240 replaced with A, G, I, S, T, M, or V; Q241replaced with N; L242 replaced with A, G, I, S, T, M, or V; A243replaced with G, I, L, S, T, M, or V; I244 replaced with A, G, L, S, T,M, or V; R246 replaced with H, or K; E247 replaced with D; N248 replacedwith Q; A249 replaced with G, I, L, S, T, M, or V; Q250 replaced with N;I251 replaced with A, G, L, S, T, M, or V; S252 replaced with A, G, I,L, T, M, or V; L253 replaced with A, G, I, S, T, M, or V; D254 replacedwith E; G255 replaced with A, I, L, S, T, M, or V; D256 replaced with E;V257 replaced with A, G, I, L, S, T, or M; T258 replaced with A, G, I,L, S, M, or V; F259 replaced with W, or Y; F260 replaced with W, or Y;G261 replaced with A, I, L, S, T, M, or V; A262 replaced with G, I, L,S, T, M, or V; L263 replaced with A, G, I, S, T, M, or V; K264 replacedwith H, or R; L265 replaced with A, G, I, S, T, M, or V; and/or L266replaced with A, G, I, S, T, M, or V. Polynucleotides encoding thesepolypeptides are also encompassed by the invention. The resultingNeutrokine-alpha proteins of the invention may be routinely screened forNeutrokine-alpha and/or Neutrokine-alphaSV functional activity and/orphysical properties (such as, for example, enhanced or reduced stabilityand/or solubility). Preferably, the resulting proteins of the inventionhave an increased and/or a decreased Neutrokine-alpha and/orNeutrokine-alphaSV functional activity. More preferably, the resultingNeutrokine-alpha and/or Neutrokine-alphaSV proteins of the inventionhave more than one increased and/or decreased Neutrokine-alpha and/orNeutrokine-alpha SV functional activity and/or physical property.

In another embodiment, site directed changes at the amino acid level ofNeutrokine-alpha can be made by replacing a particular amino acid with aconservative substitution. Preferred conservative substitution mutationsof the Neutrokine-alpha amino acid sequence provided in SEQ ID NO:23include: R1 replaced with H, or K; V2 replaced with A, G, I, L, S, T, orM; V3 replaced with A, G, I, L, S, T, or M; D4 replaced with E; L5replaced with A, G, I, S, T, M, or V; S6 replaced with A, G, I, L, T, M,or V; A7 replaced with G, I, L, S, T, M, or V; A10 replaced with G, I,L, S, T, M, or V; L13 replaced with A, G, I, S, T, M, or V; G15 replacedwith A, I, L, S, T, M, or V; R17 replaced with H, or K; H18 replacedwith K, or R; S19 replaced with A, G, I, L, T, M, or V; Q20 replacedwith N; H21 replaced with K, or R; D22 replaced with E; D23 replacedwith E; N24 replaced with Q; G25 replaced with A, I, L, S, T, M, or V;M26 replaced with A, G, I, L, S, T, or V; N27 replaced with Q; L28replaced with A, G, I, S, T, M, or V; R29 replaced with H, or K; N30replaced with Q; R31 replaced with H, or K; T32 replaced with A, G, I,L, S, M, or V; Y33 replaced with F, or W; T34 replaced with A, G, I, L,S, M, or V; F35 replaced with W, or Y; V36 replaced with A, G, I, L, S,T, or M; W38 replaced with F, or Y; L39 replaced with A, G, I, S, T, M,or V; L40 replaced with A, G, I, S, T, M, or V; S41 replaced with A, G,I, L, T, M, or V; F42 replaced with W, or Y; K43 replaced with H, or R;R44 replaced with H, or K; G45 replaced with A, I, L, S, T, M, or V; N46replaced with Q; A47 replaced with G, I, L, S, T, M, or V; L48 replacedwith A, G, I, S, T, M, or V; E49 replaced with D; E50 replaced with D;K51 replaced with H, or R; E52 replaced with D; N53 replaced with Q; K54replaced with H, or R; I55 replaced with A, G, L, S, T, M, or V; V56replaced with A, G, I, L, S, T, or M; V57 replaced with A, G, I, L, S,T, or M; R58 replaced with H, or K; Q59 replaced with N; T60 replacedwith A, G, I, L, S, M, or V; G61 replaced with A, I, L, S, T, M, or V;Y62 replaced with F, or W; F63 replaced with W, or Y; F64 replaced withW, or Y; I65 replaced with A, G, L, S, T, M, or V; Y66 replaced with F,or W; S67 replaced with A, G, I, L, T, M, or V; Q68 replaced with N; V69replaced with A, G, I, L, S, T, or M; L70 replaced with A, G, I, S, T,M, or V; Y71 replaced with F, or W; T72 replaced with A, G, I, L, S, M,or V; D73 replaced with E; I75 replaced with A, G, L, S, T, M, or V; F76replaced with W, or Y; A77 replaced with G, I, L, S, T, M, or V; M78replaced with A, G, I, L, S, T, or V; G79 replaced with A, I, L, S, T,M, or V; H80 replaced with K, or R; V81 replaced with A, G, I, L, S, T,or M; I82 replaced with A, G, L, S, T, M, or V; Q83 replaced with N; R84replaced with H, or K; K85 replaced with H, or R; K86 replaced with H,or R; V87 replaced with A, G, I, L, S, T, or M; H88 replaced with K, orR; V89 replaced with A, G, I, L, S, T, or M; F90 replaced with W, or Y;G91 replaced with A, I, L, S, T, M, or V; D92 replaced with E; E93replaced with D; L94 replaced with A, G, I, S, T, M, or V; S95 replacedwith A, G, I, L, T, M, or V; L96 replaced with A, G, I, S, T, M, or V;V97 replaced with A, G, I, L, S, T, or M; T98 replaced with A, G, I, L,S, M, or V; L99 replaced with A, G, I, S, T, M, or V; F100 replaced withW, or Y; R101 replaced with H, or K; I103 replaced with A, G, L, S, T,M, or V; Q104 replaced with N; N105 replaced with Q; M106 replaced withA, G, I, L, S, T, or V; K108 replaced with H, or R; T109 replaced withA, G, I, L, S, M, or V; L110 replaced with A, G, I, S, T, M, or V; N112replaced with Q; N113 replaced with Q; S114 replaced with A, G, I, L, T,M, or V; Y116 replaced with F, or W; S117 replaced with A, G, I, L, T,M, or V; A118 replaced with G, I, L, S, T, M, or V; G119 replaced withA, I, L, S, T, M, or V; I120 replaced with A, G, L, S, T, M, or V; A121replaced with G, I, L, S, T, M, or V; R122 replaced with H, or K; L123replaced with A, G, I, S, T, M, or V; E124 replaced with D; E125replaced with D; G126 replaced with A, I, L, S, T, M, or V; D127replaced with E; E128 replaced with D; I129 replaced with A, G, L, S, T,M, or V; Q130 replaced with N; L131 replaced with A, G, I, S, T, M, orV; A132 replaced with G, I, L, S, T, M, or V; I133 replaced with A, G,L, S, T, M, or V; R135 replaced with H, or K; E136 replaced with D; N137replaced with Q; A138 replaced with G, I, L, S, T, M, or V; Q139replaced with N; I140 replaced with A, G, L, S, T, M, or V; S141replaced with A, G, I, L, T, M, or V; R142 replaced with H, or K; N143replaced with Q; G144 replaced with A, I, L, S, T, M, or V; D145replaced with E; D146 replaced with E; T147 replaced with A, G, I, L, S,M, or V; F148 replaced with W, or Y; F149 replaced with W, or Y; G150replaced with A, I, L, S, T, M, or V; A151 replaced with G, I, L, S, T,M, or V; L152 replaced with A, G, I, S, T, M, or V; K153 replaced withH, or R; L154 replaced with A, G, I, S, T, M, or V; and/or L155 replacedwith A, G, I, S, T, M, or V. Polynucleotides encoding these polypeptidesare also encompassed by the invention. The resulting Neutrokine-alphaproteins of the invention may be routinely screened for Neutrokine-alphaand/or Neutrokine-alphaSV functional activity and/or physical properties(such as, for example, enhanced or reduced stability and/or solubility).Preferably, the resulting proteins of the invention have an increasedand/or a decreased Neutrokine-alpha and/or Neutrokine-alphaSV functionalactivity. More preferably, the resulting Neutrokine-alpha and/orNeutrokine-alphaSV proteins of the invention have more than oneincreased and/or decreased Neutrokine-alpha and/or Neutrokine-alpha SVfunctional activity and/or physical property.

In another embodiment, site directed changes at the amino acid level ofNeutrokine-alpha can be made by replacing a particular amino acid with aconservative substitution. Preferred conservative substitution mutationsof the Neutrokine-alpha amino acid sequence provided in SEQ ID NO:38include: M1 replaced with A, G, I, L, S, T, or V; D2 replaced with E; E3replaced with D; S4 replaced with A, G, I, L, T, M, or V; A5 replacedwith G, I, L, S, T, M, or V; K6 replaced with H, or R; T7 replaced withA, G, I, L, S, M, or V; L8 replaced with A, G, I, S, T, M, or V; L13replaced with A, G, I, S, T, M, or V; F15 replaced with W, or Y; S17replaced with A, G, I, L, T, M, or V; E18 replaced with D; K19 replacedwith H, or R; G20 replaced with A, I, L, S, T, M, or V; E21 replacedwith D; D22 replaced with E; M23 replaced with A, G, I, L, S, T, or V;K24 replaced with H, or R; V25 replaced with A, G, I, L, S, T, or M; G26replaced with A, I, L, S, T, M, or V; Y27 replaced with F, or W; D28replaced with E; I30 replaced with A, G, L, S, T, M, or V; T31 replacedwith A, G, I, L, S, M, or V; Q33 replaced with N; K34 replaced with H,or R; E35 replaced with D; E36 replaced with D; G37 replaced with A, I,L, S, T, M, or V; A38 replaced with G, I, L, S, T, M, or V; W39 replacedwith F, or Y; F40 replaced with W, or Y; G41 replaced with A, I, L, S,T, M, or V; I42 replaced with A, G, L, S, T, M, or V; R44 replaced withH, or K; D45 replaced with E; G46 replaced with A, I, L, S, T, M, or V;R47 replaced with H, or K; L48 replaced with A, G, I, S, T, M, or V; L49replaced with A, G, I, S, T, M, or V; A50 replaced with G, I, L, S, T,M, or V; A51 replaced with G, I, L, S, T, M, or V; T52 replaced with A,G, I, L, S, M, or V; L53 replaced with A, G, I, S, T, M, or V; L54replaced with A, G, I, S, T, M, or V; L55 replaced with A, G, I, S, T,M, or V; A56 replaced with G, I, L, S, T, M, or V; L57 replaced with A,G, I, S, T, M, or V; L58 replaced with A, G, I, S, T, M, or V; S59replaced with A, G, I, L, T, M, or V; S60 replaced with A, G, I, L, T,M, or V; S61 replaced with A, G, I, L, T, M, or V; F62 replaced with W,or Y; T63 replaced with A, G, I, L, S, M, or V; A64 replaced with G, I,L, S, T, M, or V; M65 replaced with A, G, I, L, S, T, or V; S66 replacedwith A, G, I, L, T, M, or V; L67 replaced with A, G, I, S, T, M, or V;Y68 replaced with F, or W; Q69 replaced with N; L70 replaced with A, G,I, S, T, M, or V; A71 replaced with G, I, L, S, T, M, or V; A72 replacedwith G, I, L, S, T, M, or V; L73 replaced with A, G, I, S, T, M, or V;Q74 replaced with N; A75 replaced with G, I, L, S, T, M, or V; D76replaced with E; L77 replaced with A, G, I, S, T, M, or V; M78 replacedwith A, G, I, L, S, T, or V; N79 replaced with Q; L80 replaced with A,G, I, S, T, M, or V; R81 replaced with H, or K; M82 replaced with A, G,I, L, S, T, or V; E83 replaced with D; L84 replaced with A, G, I, S, T,M, or V; Q85 replaced with N; S86 replaced with A, G, I, L, T, M, or V;Y87 replaced with F, or W; R88 replaced with H, or K; G89 replaced withA, I, L, S, T, M, or V; S90 replaced with A, G, I, L, T, M, or V; A91replaced with G, I, L, S, T, M, or V; T92 replaced with A, G, I, L, S,M, or V; A94 replaced with G, I, L, S, T, M, or V; A95 replaced with G,I, L, S, T, M, or V; A96 replaced with G, I, L, S, T, M, or V; G97replaced with A, I, L, S, T, M, or V; A98 replaced with G, I, L, S, T,M, or V; E100 replaced with D; L101 replaced with A, G, I, S, T, M, orV; T102 replaced with A, G, I, L, S, M, or V; A103 replaced with G, I,L, S, T, M, or V; G104 replaced with A, I, L, S, T, M, or V; V105replaced with A, G, I, L, S, T, or M; K106 replaced with H, or R; L107replaced with A, G, I, S, T, M, or V; L108 replaced with A, G, I, S, T,M, or V; T109 replaced with A, G, I, L, S, M, or V; A111 replaced withG, I, L, S, T, M, or V; A112 replaced with G, I, L, S, T, M, or V; R114replaced with H, or K; H116 replaced with K, or R; N117 replaced with Q;S118 replaced with A, G, I, L, T, M, or V; S119 replaced with A, G, I,L, T, M, or V; R120 replaced with H, or K; G121 replaced with A, I, L,S, T, M, or V; H122 replaced with K, or R; R123 replaced with H, or K;N124 replaced with Q; R125 replaced with H, or K; R126 replaced with H,or K; A127 replaced with G, I, L, S, T, M, or V; F128 replaced with W,or Y; Q129 replaced with N; G130 replaced with A, I, L, S, T, M, or V;E132 replaced with D; E133 replaced with D; T134 replaced with A, G, I,L, S, M, or V; E135 replaced with D; Q136 replaced with N; D137 replacedwith E; V138 replaced with A, G, I, L, S, T, or M; D139 replaced with E;L140 replaced with A, G, I, S, T, M, or V; S141 replaced with A, G, I,L, T, M, or V; A142 replaced with G, I, L, S, T, M, or V; A145 replacedwith G, I, L, S, T, M, or V; L148 replaced with A, G, I, S, T, M, or V;G150 replaced with A, I, L, S, T, M, or V; R152 replaced with H, or K;H153 replaced with K, or R; S154 replaced with A, G, I, L, T, M, or V;Q155 replaced with N; H156 replaced with K, or R; D157 replaced with E;D158 replaced with E; N159 replaced with Q; G160 replaced with A, I, L,S, T, M, or V; M161 replaced with A, G, I, L, S, T, or V; N162 replacedwith Q; L163 replaced with A, G, I, S, T, M, or V; R164 replaced with H,or K; N165 replaced with Q; I166 replaced with A, G, L, S, T, M, or V;I167 replaced with A, G, L, S, T, M, or V; Q168 replaced with N; D169replaced with E; L171 replaced with A, G, I, S, T, M, or V; Q172replaced with N; L173 replaced with A, G, I, S, T, M, or V; I174replaced with A, G, L, S, T, M, or V; A175 replaced with G, I, L, S, T,M, or V; D176 replaced with E; S177 replaced with A, G, I, L, T, M, orV; D178 replaced with E; T179 replaced with A, G, I, L, S, M, or V; A181replaced with G, I, L, S, T, M, or V; L182 replaced with A, G, I, S, T,M, or V; E183 replaced with D; E184 replaced with D; K185 replaced withH, or R; E186 replaced with D; N187 replaced with Q; K188 replaced withH, or R; I189 replaced with A, G, L, S, T, M, or V; V190 replaced withA, G, I, L, S, T, or M; V191 replaced with A, G, I, L, S, T, or M; R192replaced with H, or K; Q193 replaced with N; T194 replaced with A, G, I,L, S, M, or V; G195 replaced with A, I, L, S, T, M, or V; Y196 replacedwith F, or W; F197 replaced with W, or Y; F198 replaced with W, or Y;I199 replaced with A, G, L, S, T, M, or V; Y200 replaced with F, or W;S201 replaced with A, G, I, L, T, M, or V; Q202 replaced with N; V203replaced with A, G, I, L, S, T, or M; L204 replaced with A, G, I, S, T,M, or V; Y205 replaced with F, or W; T206 replaced with A, G, I, L, S,M, or V; D207 replaced with E; I209 replaced with A, G, L, S, T, M, orV; F210 replaced with W, or Y; A211 replaced with G, I, L, S, T, M, orV; M212 replaced with A, G, I, L, S, T, or V; G213 replaced with A, I,L, S, T, M, or V; H214 replaced with K, or R; V215 replaced with A, G,I, L, S, T, or M; I216 replaced with A, G, L, S, T, M, or V; Q217replaced with N; R218 replaced with H, or K; K219 replaced with H, or R;K220 replaced with H, or R; V221 replaced with A, G, I, L, S, T, or M;H222 replaced with K, or R; V223 replaced with A, G, I, L, S, T, or M;F224 replaced with W, or Y; G225 replaced with A, I, L, S, T, M, or V;D226 replaced with E; E227 replaced with D; L228 replaced with A, G, I,S, T, M, or V; S229 replaced with A, G, I, L, T, M, or V; L230 replacedwith A, G, I, S, T, M, or V; V231 replaced with A, G, I, L, S, T, or M;T232 replaced with A, G, I, L, S, M, or V; L233 replaced with A, G, I,S, T, M, or V; F234 replaced with W, or Y; R235 replaced with H, or K;I237 replaced with A, G, L, S, T, M, or V; Q238 replaced with N; N239replaced with Q; M240 replaced with A, G, I, L, S, T, or V; K242replaced with H, or R; T243 replaced with A, G, I, L, S, M, or V; L244replaced with A, G, I, S, T, M, or V; N246 replaced with Q; N247replaced with Q; S248 replaced with A, G, I, L, T, M, or V; Y250replaced with F, or W; S251 replaced with A, G, I, L, T, M, or V; A252replaced with G, I, L, S, T, M, or V; G253 replaced with A, I, L, S, T,M, or V; I254 replaced with A, G, L, S, T, M, or V; A255 replaced withG, I, L, S, T, M, or V; R256 replaced with H, or K; L257 replaced withA, G, I, S, T, M, or V; E258 replaced with D; E259 replaced with D; G260replaced with A, I, L, S, T, M, or V; D261 replaced with E; E262replaced with D; I263 replaced with A, G, L, S, T, M, or V; Q264replaced with N; L265 replaced with A, G, I, S, T, M, or V; A266replaced with G, I, L, S, T, M, or V; I267 replaced with A, G, L, S, T,M, or V; R269 replaced with H, or K; E270 replaced with D; N271 replacedwith Q; A272 replaced with G, I, L, S, T, M, or V; Q273 replaced with N;I274 replaced with A, G, L, S, T, M, or V; 5275 replaced with A, G, I,L, T, M, or V; R276 replaced with H, or K; N277 replaced with Q; G278replaced with A, I, L, S, T, M, or V; D279 replaced with E; D280replaced with E; T281 replaced with A, G, I, L, S, M, or V; F282replaced with W, or Y; F283 replaced with W, or Y; G284 replaced with A,I, L, S, T, M, or V; A285 replaced with G, I, L, S, T, M, or V; L286replaced with A, G, I, S, T, M, or V; K287 replaced with H, or R; L288replaced with A, G, I, S, T, M, or V; and/or L289 replaced with A, G, I,S, T, M, or V. Polynucleotides encoding these polypeptides are alsoencompassed by the invention. The resulting Neutrokine-alpha proteins ofthe invention may be routinely screened for Neutrokine-alpha and/orNeutrokine-alphaSV functional activity and/or physical properties (suchas, for example, enhanced or reduced stability and/or solubility).Preferably, the resulting proteins of the invention have an increasedand/or a decreased Neutrokine-alpha and/or Neutrokine-alphaSV functionalactivity. More preferably, the resulting Neutrokine-alpha and/orNeutrokine-alphaSV proteins of the invention have more than oneincreased and/or decreased Neutrokine-alpha and/or Neutrokine-alpha SVfunctional activity and/or physical property.

Amino acids in the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the present invention that are essential for functioncan be identified by methods known in the art, such as site-directedmutagenesis or alanine-scanning mutagenesis (Cunningham and Wells,Science 244:1081-1085 (1989)). The latter procedure introduces singlealanine mutations at every residue in the molecule. The resulting mutantmolecules are then tested for functional activity, such ligand bindingand the ability to stimulate lymphocyte (e.g., B cell) as, for example,proliferation, differentiation, and/or activation.

Of special interest are substitutions of charged amino acids with othercharged or neutral amino acids which may produce proteins with highlydesirable improved characteristics, such as less aggregation.Aggregation may not only reduce activity but also be problematic whenpreparing pharmaceutical formulations, because aggregates can beimmunogenic (Pinckard et al., Clin. Exp. Immunol. 2:331-340 (1967);Robbins et al., Diabetes 36: 838-845 (1987); Cleland et al., Crit. Rev.Therapeutic Drug Carrier Systems 10:307-377 (1993).

In another embodiment, the invention provides for polypeptides havingamino acid sequences containing non-conservative substitutions of theamino acid sequence provided in SEQ ID NO:2. For example,non-conservative substitutions of the Neutrokine-alpha protein sequenceprovided in SEQ ID NO:2 include: M1 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; D2 replaced with H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; D3 replaced with H, K, R, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; S4 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; T5 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E6replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;R7 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E8 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; Q9 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; S10 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R11replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L12replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T13 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; S14 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; C15 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, or P; L16 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; K17 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F,W, Y, P, or C; K18 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F,W, Y, P, or C; R19 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F,W, Y, P, or C; E20 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; E21 replaced with H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; M22 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; K23 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; L24 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K25replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E26replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;C27 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y,or P; V28 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S29replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I30 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L31 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; P32 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, or C; R33 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; K34 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; E35 replaced with H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; S36 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; P37 replaced with D, E, H, K, R, A, G, I, L, S, T, M,V, N, Q, F, W, Y, or C; S38 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; V39 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R40replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S41replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S42 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; K43 replaced with D, E, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; D44 replaced with H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G45 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; K46 replaced with D, E, A, G, I, L, S, T, M,V, N, Q, F, W, Y, P, or C; L47 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; L48 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A49replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A50 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; T51 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; L52 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; L53 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L54replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A55 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L56 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; L57 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; S58 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C59replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orP; C60 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W,Y, or P; L61 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T62replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V63 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; V64 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; S65 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; F66 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V,P, or C; Y67 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V,P, or C; Q68 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W,Y, P, or C; V69 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A70replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A71 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L72 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; Q73 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, F, W, Y, P, or C; G74 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; D75 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F,W, Y, P, or C; L76 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;A77 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S78 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; L79 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; R80 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; A81 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; E82 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; L83 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; Q84 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; G85 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H86replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H87replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A88replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E89 replaced withH, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K90 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L91 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; P92 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A93 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; G94 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; A95 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; G96 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A97replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P98 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K99 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A100 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; G101 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; L102 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; E103 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; E104 replaced with H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; A105 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; P106 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F,W, Y, or C; A107 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;V108 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T109 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; A110 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; G111 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; L112 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;K113 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;I114 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F115 replacedwith D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E116 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P117replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; P118 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W,Y, or C; A119 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P120replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; G121 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E122replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;G123 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N124 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S125replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S126 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Q127 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; N128 replaced with D, E, H, K,R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S129 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; R130 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; N131 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, F, W, Y, P, or C; K132 replaced with D, E, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; R133 replaced with D, E, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; A134 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; V135 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; Q136 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; G137 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P138replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; E139 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; E140 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; T141 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V142replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T143 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Q144 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; D145 replaced with H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C146 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; L147 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; Q148 replaced with D, E, H, K, R, A,G, I, L, S, T, M, V, F, W, Y, P, or C; L149 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; I150 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; A151 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D152replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;S153 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E154 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T155replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P156 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; T157replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I158 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Q159 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; K160 replaced with D, E, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G161 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; S162 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; Y163 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; T164 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;F165 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C;V166 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P167 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; W168replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L169replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L170 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; S171 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; F172 replaced with D, E, H, K, R, N, Q, A, G, I,L, S, T, M, V, P, or C; K173 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; R174 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; G175 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; S176 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A177replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L178 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; E179 replaced with H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E180 replaced with H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K181 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E182 replaced with H, K, R,A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N183 replaced with D, E,H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K184 replaced with D,E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I185 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; L186 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; V187 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; K188 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; E189 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; T190 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G191replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y192 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F193 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F194 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; I195 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Y196 replaced with D, E, H, K, R,N, Q, A, G, I, L, S, T, M, V, P, or C; G197 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; Q198 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, F, W, Y, P, or C; V199 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; L200 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;Y201 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C;T202 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D203 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K204replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T205replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y206 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; A207 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; M208 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; G209 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; H210 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; L211 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I212replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q213 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R214 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K215 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K216 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V217 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; H218 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V219 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; F220 replaced with D, E, H, K, R, N, Q, A,G, I, L, S, T, M, V, P, or C; G221 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; D222 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; E223 replaced with H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; L224 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; S225 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L226replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V227 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; T228 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; L229 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; F230 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V,P, or C; R231 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; C232 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, or P; I233 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;Q234 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; N235 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; M236 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P237replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; E238 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; T239 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L240replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P241 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; N242replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;N243 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; S244 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C245replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orP; Y246 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, orC; S247 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A248replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G249 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; I250 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; A251 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; K252 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; L253 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E254replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E255 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; G256 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D257replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E258 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; L259 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q260replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;L261 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A262 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; 1263 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; P264 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, or C; R265 replaced with D, E, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; E266 replaced with H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; N267 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; A268 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; Q269 replaced with D, E, H, K, R, A, G, I, L,S, T, M, V, F, W, Y, P, or C; I270 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; S271 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L272 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D273 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G274replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D275 replaced withH, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V276 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; T277 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; F278 replaced with D, E, H, K, R, N, Q, A,G, I, L, S, T, M, V, P, or C; F279 replaced with D, E, H, K, R, N, Q, A,G, I, L, S, T, M, V, P, or C; G280 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; A281 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L282 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K283 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L284 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; and/or L285 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C. Polynucleotides encoding thesepolypeptides are also encompassed by the invention. The resultingNeutrokine-alpha proteins of the invention may be routinely screened forNeutrokine-alpha and/or Neutrokine-alphaSV functional activities and/orphysical properties (such as, for example, enhanced or reduced stabilityand/or solubility) described throughout the specification and known inthe art. Preferably, the resulting proteins of the invention have anincreased and/or a decreased Neutrokine-alpha and/or Neutrokine-alphaSVfunctional activity. More preferably, the resulting Neutrokine-alphaand/or Neutrokine-alphaSV proteins of the invention have more than oneincreased and/or decreased Neutrokine-alpha and/or Neutrokine-alphaSVfunctional activity and/or physical property.

In an additional embodiment, Neutrokine-alpha polypeptides of theinvention comprise, or alternatively consist of, more than one aminoacid (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30 and 50) replaced withthe substituted amino acids as described above (either conservative ornonconservative).

In another embodiment of the invention, non-conservative substitutionsof the Neutrokine-alphaSV protein sequence provided in SEQ ID NO:19include: M1 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D2replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;D3 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; S4 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T5 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; E6 replaced with H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R7 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E8 replaced with H, K, R,A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q9 replaced with D, E,H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S10 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; R11 replaced with D, E, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; L12 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; T13 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; S14 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C15replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orP; L16 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K17 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K18 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R19 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E20 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E21replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;M22 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K23 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L24 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; K25 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E26 replaced with H, K, R,A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C27 replaced with D, E,H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; V28 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; S29 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; I30 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; L31 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P32replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; R33 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; K34 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; E35 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; S36 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P37replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; S38 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V39 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; R40 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S41 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; S42 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; K43 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F,W, Y, P, or C; D44 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; G45 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; K46 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; L47 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L48 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; A49 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; A50 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; T51 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L52 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L53 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; L54 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; A55 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; L56 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L57 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S58 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; C59 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; C60 replaced with D,E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; L61 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; T62 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; V63 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; V64 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;S65 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F66 replacedwith D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Y67 replacedwith D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q68 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V69replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A70 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; A71 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; L72 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; Q73 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W,Y, P, or C; G74 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D75replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;L76 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A77 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; S78 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; L79 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; R80 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F,W, Y, P, or C; A81 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;E82 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; L83 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q84 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G85replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H86 replaced withD, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H87 replaced withD, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A88 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; E89 replaced with H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K90 replaced with D, E, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L91 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; P92 replaced with D, E, H, K, R, A, G, I, L,S, T, M, V, N, Q, F, W, Y, or C; A93 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; G94 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; A95 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G96 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; A97 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; P98 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, or C; K99 replaced with D, E, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; A100 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; G101 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; L102 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E103replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E104 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; A105 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P106replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; A107 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V108replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T109 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; A110 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; G111 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; L112 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K113replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I114replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F115 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E116 replaced withH, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P117 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; P118replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; A119 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P120replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; G121 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E122replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;G123 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N124 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S125replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S126 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Q127 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; N128 replaced with D, E, H, K,R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S129 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; R130 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; N131 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, F, W, Y, P, or C; K132 replaced with D, E, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; R133 replaced with D, E, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; A134 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; V135 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; Q136 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; G137 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P138replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; E139 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; E140 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; T141 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G142replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S143 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Y144 replaced with D, E, H, K, R,N, Q, A, G, I, L, S, T, M, V, P, or C; T145 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; F146 replaced with D, E, H, K, R, N, Q, A, G, I,L, S, T, M, V, P, or C; V147 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; P148 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, or C; W149 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T,M, V, P, or C; L150 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L151 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S152 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; F153 replaced with D, E, H,K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; K154 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R155 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G156 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; S157 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; A158 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L159 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E160 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E161replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;K162 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E163 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; N164 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; K165 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; I166 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L167replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V168 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; K169 replaced with D, E, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; E170 replaced with H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T171 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; G172 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; Y173 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; F174 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; F175 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; I176 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;Y177 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C;G178 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q179 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V180replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L181 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Y182 replaced with D, E, H, K, R,N, Q, A, G, I, L, S, T, M, V, P, or C; T183 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; D184 replaced with H, K, R, A, G, I, L, S, T, M,V, N, Q, F, W, Y, P, or C; K185 replaced with D, E, A, G, I, L, S, T, M,V, N, Q, F, W, Y, P, or C; T186 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; Y187 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; A188 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;M189 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G190 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; H191 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L192 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; I193 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; Q194 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V,F, W, Y, P, or C; R195 replaced with D, E, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; K196 replaced with D, E, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; K197 replaced with D, E, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; V198 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; H199 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; V200 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F201replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G202replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D203 replaced withH, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E204 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L205replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S206 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L207 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; V208 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; T209 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L210replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F211 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R212 replaced withD, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C213 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; I214replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q215 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; N216 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; M217replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P218 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E219replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;T220 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L221 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; P222 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; N223 replaced with D,E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; N224 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S225 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; C226 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Y227 replaced with D,E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S228 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; A229 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; G230 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; I231 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A232replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K233 replaced withD, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L234 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; E235 replaced with H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E236 replaced with H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G237 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; D238 replaced with H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; E239 replaced with H, K, R, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; L240 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; Q241 replaced with D, E, H, K, R, A, G, I, L, S, T,M, V, F, W, Y, P, or C; L242 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; A243 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I244replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P245 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; R246replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E247replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;N248 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; A249 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q250replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;I251 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S252 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; L253 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; D254 replaced with H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; G255 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; D256 replaced with H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; V257 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; T258 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F259replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F260replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G261replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A262 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L263 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; K264 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; L265 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; and/or L266 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC. Polynucleotides encoding these polypeptides are also encompassed bythe invention. The resulting Neutrokine-alpha proteins of the inventionmay be routinely screened for Neutrokine-alpha and/or Neutrokine-alphaSVfunctional activities and/or physical properties (such as, for example,enhanced or reduced stability and/or solubility) described throughoutthe specification and known in the art. Preferably, the resultingproteins of the invention have an increased and/or a decreasedNeutrokine-alpha and/or Neutrokine-alphaSV functional activity. Morepreferably, the resulting Neutrokine-alpha and/or Neutrokine-alphaSVproteins of the invention have more than one increased and/or decreasedNeutrokine-alpha and/or Neutrokine-alphaSV functional activity and/orphysical property.

In an additional embodiment, Neutrokine-alpha polypeptides of theinvention comprise, or alternatively consist of, more than one aminoacid (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30 and 50) replaced withthe substituted amino acids as described above (either conservative ornonconservative).

For example, preferred non-conservative substitutions of theNeutrokine-alpha protein sequence provided in SEQ ID NO:23 include: R1replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V2replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V3 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; D4 replaced with H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; L5 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; S6 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; A7 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P8replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; P9 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W,Y, or C; A10 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P11replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; C12 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W,Y, or P; L13 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P14replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; G15 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C16 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; R17replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H18replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S19replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q20 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; H21 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D22 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D23replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;N24 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; G25 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; M26 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; N27 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L28 replaced with D, E,H, K, R, N, Q, F, W, Y, P, or C; R29 replaced with D, E, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; N30 replaced with D, E, H, K, R, A, G,I, L, S, T, M, V, F, W, Y, P, or C; R31 replaced with D, E, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; T32 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; Y33 replaced with D, E, H, K, R, N, Q, A, G, I, L,S, T, M, V, P, or C; T34 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; F35 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P,or C; V36 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P37replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; W38 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, orC; L39 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L40 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; S41 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; F42 replaced with D, E, H, K, R, N, Q, A,G, I, L, S, T, M, V, P, or C; K43 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; R44 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; G45 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; N46 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V,F, W, Y, P, or C; A47 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; L48 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E49 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E50replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;K51 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E52 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; N53 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; K54 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; I55 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V56replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V57 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; R58 replaced with D, E, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; Q59 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; T60 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; G61 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; Y62 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; F63 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; F64 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; I65 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y66replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S67replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q68 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V69 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; L70 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; Y71 replaced with D, E, H, K, R, N, Q, A,G, I, L, S, T, M, V, P, or C; T72 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; D73 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; P74 replaced with D, E, H, K, R, A, G, I, L, S, T, M,V, N, Q, F, W, Y, or C; I75 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; F76 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V,P, or C; A77 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; M78replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G79 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; H80 replaced with D, E, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; V81 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; I82 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; Q83 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W,Y, P, or C; R84 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W,Y, P, or C; K85 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W,Y, P, or C; K86 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W,Y, P, or C; V87 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H88replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V89replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F90 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G91 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; D92 replaced with H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E93 replaced with H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L94 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; S95 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; L96 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;V97 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T98 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; L99 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; F100 replaced with D, E, H, K, R, N, Q, A,G, I, L, S, T, M, V, P, or C; R101 replaced with D, E, A, G, I, L, S, T,M, V, N, Q, F, W, Y, P, or C; C102 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, or P; I103 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; Q104 replaced with D, E, H, K, R, A, G, I, L, S, T,M, V, F, W, Y, P, or C; N105 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, F, W, Y, P, or C; M106 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; P107 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, or C; K108 replaced with D, E, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; T109 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; L110 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P111replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; N112 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P,or C; N113 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y,P, or C; S114 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C115replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orP; Y116 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, orC; S117 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A118replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G119 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; I120 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; A121 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; R122 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; L123 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E124replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E125 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; G126 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D127replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E128 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; I129 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q130replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;L131 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A132 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; 1133 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; P134 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, or C; R135 replaced with D, E, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; E136 replaced with H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; N137 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; A138 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; Q139 replaced with D, E, H, K, R, A, G, I, L,S, T, M, V, F, W, Y, P, or C; I140 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; S141 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;R142 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;N143 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; G144 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D145replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;D146 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; T147 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F148replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F149replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G150replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A151 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L152 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; K153 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; L154 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; and/or L155 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC. Polynucleotides encoding these polypeptides are also encompassed bythe invention. The resulting Neutrokine-alpha proteins of the inventionmay be routinely screened for Neutrokine-alpha and/or Neutrokine-alphaSVfunctional activities and/or physical properties (such as, for example,enhanced or reduced stability and/or solubility) described throughoutthe specification and known in the art. Preferably, the resultingproteins of the invention have an increased and/or a decreasedNeutrokine-alpha and/or Neutrokine-alphaSV functional activity. Morepreferably, the resulting Neutrokine-alpha and/or Neutrokine-alphaSVproteins of the invention have more than one increased and/or decreasedNeutrokine-alpha and/or Neutrokine-alphaSV functional activity and/orphysical property.

In an additional embodiment, Neutrokine-alpha polypeptides of theinvention comprise, or alternatively consist of, more than one aminoacid (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30 and 50) replaced withthe substituted amino acids as described above (either conservative ornonconservative).

For example, preferred non-conservative substitutions of theNeutrokine-alpha protein sequence provided in SEQ ID NO:38 include: M1replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D2 replaced with H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E3 replaced withH, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S4 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; A5 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; K6 replaced with D, E, A, G, I, L, S, T, M,V, N, Q, F, W, Y, P, or C; T7 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; L8 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P9replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; P10 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W,Y, or C; P11 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, or C; C12 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V,N, Q, F, W, Y, or P; L13 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; C14 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F,W, Y, or P; F15 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M,V, P, or C; C16 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, or P; S17 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; E18 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; K19 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; G20 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E21replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;D22 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; M23 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K24 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V25 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; G26 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; Y27 replaced with D, E, H, K, R, N, Q, A,G, I, L, S, T, M, V, P, or C; D28 replaced with H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; P29 replaced with D, E, H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, or C; I30 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; T31 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; P32 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, or C; Q33 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V,F, W, Y, P, or C; K34 replaced with D, E, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; E35 replaced with H, K, R, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; E36 replaced with H, K, R, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; G37 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; A38 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W39replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F40replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G41replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I42 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; C43 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; R44 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D45 replaced with H, K, R,A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G46 replaced with D, E,H, K, R, N, Q, F, W, Y, P, or C; R47 replaced with D, E, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; L48 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; L49 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; A50 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A51 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; T52 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; L53 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; L54 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L55 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A56 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; L57 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; L58 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; S59 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;S60 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S61 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; F62 replaced with D, E, H,K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T63 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; A64 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; M65 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;S66 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L67 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; Y68 replaced with D, E, H,K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q69 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L70 replaced with D, E,H, K, R, N, Q, F, W, Y, P, or C; A71 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; A72 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; L73 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q74 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A75replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D76 replaced withH, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L77 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; M78 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; N79 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, F, W, Y, P, or C; L80 replaced with D, E, H, K, R, N, Q,F, W, Y, P, or C; R81 replaced with D, E, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; M82 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; E83 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; L84 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q85replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;S86 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y87 replacedwith D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R88 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G89 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; S90 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; A91 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; T92 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;P93 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y,or C; A94 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A95replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A96 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; G97 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; A98 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; P99 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, or C; E100 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q,F, W, Y, P, or C; L101 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; T102 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A103replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G104 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; V105 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; K106 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; L107 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; L108 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T109replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P110 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A111replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A112 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; P113 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; R114 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P115 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; H116 replaced with D,E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N117 replaced with D,E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S118 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; S119 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; R120 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; G121 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; H122 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; R123 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; N124 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W,Y, P, or C; R125 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W,Y, P, or C; R126 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W,Y, P, or C; A127 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;F128 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C;Q129 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; G130 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P131replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; E132 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; E133 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; T134 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E135replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;Q136 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; D137 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; V138 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D139replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;L140 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S141 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; A142 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; P143 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, or C; P144 replaced with D, E, H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A145 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; P146 replaced with D, E, H, K, R, A, G, I, L,S, T, M, V, N, Q, F, W, Y, or C; C147 replaced with D, E, H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, or P; L148 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; P149 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, or C; G150 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; C151 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V,N, Q, F, W, Y, or P; R152 replaced with D, E, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; H153 replaced with D, E, A, G, I, L, S, T, M, V, N,Q, F, W, Y, P, or C; S154 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; Q155 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y,P, or C; H156 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; D157 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W,Y, P, or C; D158 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F,W, Y, P, or C; N159 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V,F, W, Y, P, or C; G160 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC; M161 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N162replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;L163 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R164 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N165 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I166replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I167 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Q168 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; D169 replaced with H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C170 replaced with D, E, H,K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; L171 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; Q172 replaced with D, E, H, K, R, A,G, I, L, S, T, M, V, F, W, Y, P, or C; L173 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; I174 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; A175 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D176replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;S177 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D178 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T179replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P180 replaced withD, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A181replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L182 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; E183 replaced with H, K, R, A, G,I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E184 replaced with H, K, R, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K185 replaced with D, E, A,G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E186 replaced with H, K, R,A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N187 replaced with D, E,H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K188 replaced with D,E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I189 replaced with D,E, H, K, R, N, Q, F, W, Y, P, or C; V190 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; V191 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; R192 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P,or C; Q193 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y,P, or C; T194 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G195replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y196 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F197 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F198 replaced withD, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; I199 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; Y200 replaced with D, E, H, K, R,N, Q, A, G, I, L, S, T, M, V, P, or C; S201 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; Q202 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, F, W, Y, P, or C; V203 replaced with D, E, H, K, R, N, Q, F, W,Y, P, or C; L204 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;Y205 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C;T206 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D207 replacedwith H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P208replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orC; I209 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F210replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; A211replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; M212 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; G213 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; H214 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; V215 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; I216 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q217replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;R218 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;K219 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;K220 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;V221 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H222 replacedwith D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V223 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; F224 replaced with D, E, H,K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G225 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; D226 replaced with H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, P, or C; E227 replaced with H, K, R, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; L228 replaced with D, E, H, K, R, N,Q, F, W, Y, P, or C; S229 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; L230 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V231replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T232 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L233 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; F234 replaced with D, E, H, K, R, N, Q, A, G, I,L, S, T, M, V, P, or C; R235 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; C236 replaced with D, E, H, K, R, A, G, I, L, S,T, M, V, N, Q, F, W, Y, or P; I237 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; Q238 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V,F, W, Y, P, or C; N239 replaced with D, E, H, K, R, A, G, I, L, S, T, M,V, F, W, Y, P, or C; M240 replaced with D, E, H, K, R, N, Q, F, W, Y, P,or C; P241 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F,W, Y, or C; K242 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W,Y, P, or C; T243 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;L244 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P245 replacedwith D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; N246replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;N247 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; S248 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C249replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, orP; Y250 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, orC; S251 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A252replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G253 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; I254 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; A255 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; R256 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y,P, or C; L257 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E258replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E259 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; G260 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D261replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;E262 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; I263 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q264replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C;L265 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A266 replacedwith D, E, H, K, R, N, Q, F, W, Y, P, or C; I267 replaced with D, E, H,K, R, N, Q, F, W, Y, P, or C; P268 replaced with D, E, H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, or C; R269 replaced with D, E, A, G, I, L,S, T, M, V, N, Q, F, W, Y, P, or C; E270 replaced with H, K, R, A, G, I,L, S, T, M, V, N, Q, F, W, Y, P, or C; N271 replaced with D, E, H, K, R,A, G, I, L, S, T, M, V, F, W, Y, P, or C; A272 replaced with D, E, H, K,R, N, Q, F, W, Y, P, or C; Q273 replaced with D, E, H, K, R, A, G, I, L,S, T, M, V, F, W, Y, P, or C; I274 replaced with D, E, H, K, R, N, Q, F,W, Y, P, or C; 5275 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C;R276 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;N277 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, orC; G278 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D279replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C;D280 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, orC; T281 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F282replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F283replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G284replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A285 replaced withD, E, H, K, R, N, Q, F, W, Y, P, or C; L286 replaced with D, E, H, K, R,N, Q, F, W, Y, P, or C; K287 replaced with D, E, A, G, I, L, S, T, M, V,N, Q, F, W, Y, P, or C; L288 replaced with D, E, H, K, R, N, Q, F, W, Y,P, or C; and/or L289 replaced with D, E, H, K, R, N, Q, F, W, Y, P, orC. Polynucleotides encoding these polypeptides are also encompassed bythe invention. The resulting Neutrokine-alpha proteins of the inventionmay be routinely screened for Neutrokine-alpha and/or Neutrokine-alphaSVfunctional activities and/or physical properties (such as, for example,enhanced or reduced stability and/or solubility) described throughoutthe specification and known in the art. Preferably, the resultingproteins of the invention have an increased and/or a decreasedNeutrokine-alpha and/or Neutrokine-alphaSV functional activity. Morepreferably, the resulting Neutrokine-alpha and/or Neutrokine-alphaSVproteins of the invention have more than one increased and/or decreasedNeutrokine-alpha and/or Neutrokine-alphaSV functional activity and/orphysical property.

In an additional embodiment, Neutrokine-alpha polypeptides of theinvention comprise, or alternatively consist of, more than one aminoacid (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30 and 50) replaced withthe substituted amino acids as described above (either conservative ornonconservative).

Replacement of amino acids can also change the selectivity of thebinding of a ligand to cell surface receptors. For example, Ostade etal., Nature 361:266-268 (1993) describes certain mutations resulting inselective binding of TNF-alpha to only one of the two known types of TNFreceptors. Since Neutrokine-alpha and Neutrokine-alphaSV are members ofthe TNF polypeptide family, mutations similar to those in TNF-alpha arelikely to have similar effects in Neutrokine-alpha and/orNeutrokine-alphaSV.

Sites that are critical for ligand-receptor binding can also bedetermined by structural analysis such as crystallization, nuclearmagnetic resonance or photoaffinity labeling (Smith et al., J. Mol.Biol. 224:899-904 (1992) and de Vos et al. Science 255:306-312 (1992)).

Since Neutrokine-alpha is a member of the TNF-related protein family, tomodulate rather than completely eliminate functional activities (e.g.,biological activities) of Neutrokine-alpha, mutations may be made insequences encoding amino acids in the TNF conserved domain, i.e., inpositions Gly-191 through Leu-284 of FIGS. 1A and 1B (SEQ ID NO:2), morepreferably in residues within this region which are not conserved inall, most or several members of the TNF family (e.g., TNF-alpha,TNF-beta, LT-beta, and Fas Ligand) (see e.g., FIGS. 2A, 2B, 2C and 2D).By making a specific mutation in Neutrokine-alpha in the position wheresuch a conserved amino acid is typically found in related TNFs, theNeutrokine-alpha mutein will act as an antagonist, thus possessingactivity for example, which inhibits lymphocyte (e.g., B cell)proliferation, differentiation, and/or activation. Accordingly,polypeptides of the present invention include Neutrokine-alpha mutants.Such Neutrokine-alpha mutants comprise, or alternatively consist of,fragments, variants or derivatives of the full-length or preferably theextracellular domain of the Neutrokine-alpha amino acid sequence shownin FIGS. 1A and 1B (SEQ ID NO:2). Polynucleotides encoding the aboveNeutrokine-alpha mutants are also encompassed by the invention.

Since Neutrokine-alphaSV is a member of the TNF-related protein family,to modulate rather than completely eliminate functional activities(e.g., biological activities) of Neutrokine-alphaSV, mutations may bemade in sequences encoding amino acids in the TNF conserved domain,i.e., in positions Gly-172 through Leu-265 of FIGS. 5A and 5B (SEQ IDNO:19), more preferably in residues within this region which are notconserved in all, most or several members of the TNF family (e.g.,TNF-alpha, TNF-beta, LT-beta, and Fas Ligand) (see e.g., FIGS. 2A, 2B,2C and 2D). By making a specific mutation in Neutrokine-alphaSV in theposition where such a conserved amino acid is typically found in relatedTNFs, the Neutrokine-alphaSV mutein will act as an antagonist, thuspossessing activity for example, which inhibits lymphocyte (e.g., Bcell) proliferation, differentiation, and/or activation. Accordingly,polypeptides of the present invention include Neutrokine-alphaSVmutants. Such Neutrokine-alphaSV mutants comprise, or alternativelyconsist of, fragments, variants or derivatives of the full-length orpreferably the extracellular domain of the Neutrokine-alphaSV amino acidsequence shown in FIGS. 5A and 5B (SEQ ID NO:19 Polynucleotides encodingthe above Neutrokine-alpha SV mutants are also encompassed by theinvention.

In addition, it will be recognized by one of ordinary skill in the artthat mutations targeted to regions of a Neutrokine-alpha polypeptide ofthe invention which encompass the nineteen amino acid residue insertionwhich is not found in the Neutrokine-alphaSV polypeptide sequence (i.e.,amino acid residues Val-142 through Lys-160 of the sequence presented inFIGS. 1A and 1B and in SEQ ID NO:2) may affect the observed functionalactivities (e.g., biological activity) of the Neutrokine-alphapolypeptide. More specifically, a partial, non-limiting andnon-exclusive list of such residues of the Neutrokine-alpha polypeptidesequence which may be targeted for mutation includes the following aminoacid residues of the Neutrokine-alpha polypeptide sequence as shown inSEQ ID NO:2: V-142; T-143; Q-144; D-145; C-146; L-147; Q-148; L-149;I-150; A-151; D-152; S-153; E-154; T-155; P-156; T-157; I-158; Q-159;and K-160.

Recombinant DNA technology known to those skilled in the art (see, forinstance, DNA shuffling supra) can be used to create novel mutantproteins or muteins including single or multiple amino acidsubstitutions, deletions, additions or fusion proteins. Such modifiedpolypeptides can show, e.g., enhanced activity or increased stability.In addition, they may be purified in higher yields and show bettersolubility than the corresponding natural polypeptide, at least undercertain purification and storage conditions.

Thus, the invention also encompasses Neutrokine-alpha and/orNeutrokine-alphaSV derivatives and analogs that have one or more aminoacid residues deleted, added, or substituted to generateNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides that are bettersuited for expression, scale up, etc., in the host cells chosen. Forexample, cysteine residues can be deleted or substituted with anotheramino acid residue in order to eliminate disulfide bridges; N-linkedglycosylation sites can be altered or eliminated to achieve, forexample, expression of a homogeneous product that is more easilyrecovered and purified from yeast hosts which are known tohyperglycosylate N-linked sites. To this end, a variety of amino acidsubstitutions at one or both of the first or third amino acid positionson any one or more of the glycosylation recognition sequences in theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides of theinvention, and/or an amino acid deletion at the second position of anyone or more such recognition sequences will prevent glycosylation of theNeutrokine-alpha and/or Neutrokine-alphaSV at the modified tripeptidesequence (see, e.g., Miyajimo et al., EMBO J. 5(6):1193-1197).

Additionally, one or more of the amino acid residues of the polypeptidesof the invention (e.g., arginine and lysine residues) may be deleted orsubstituted with another residue to eliminate undesired processing byproteases such as, for example, furins or kexins. One possible result ofsuch a mutation is that Neutrokine-alpha polypeptide of the invention isnot cleaved and released from the cell surface.

In a specific embodiment, Lys-132 and/or Arg-133 of the Neutrokine-alphasequence shown in SEQ ID NO:2 is mutated to another amino acid residue,or deleted altogether, to prevent or diminish release of the solubleform of Neutrokine-alpha from cells expressing Neutrokine-alpha. In amore specific embodiment, Lys-132 of the Neutrokine-alpha sequence shownin SEQ ID NO:2 is mutated to Ala-132. In another, nonexclusive specificembodiment, Arg-133 of the Neutrokine-alpha sequence shown in SEQ IDNO:2 is mutated to Ala-133. These mutated proteins, and/orpolynucleotides encoding these proteins have uses such as, for example,in ex vivo therapy or gene therapy, to engineer cells expressing aNeutrokine-alpha polypeptide that is retained on the surface of theengineered cells.

In a specific embodiment, Cys-146 of the Neutrokine-alpha sequence shownin SEQ ID NO:2 is mutated to another amino acid residue, or deletedaltogether, for example, to aid preventing or diminishingoligomerization of the mutant Neutrokine-alpha polypeptide whenexpressed in a expression system (essentially as described in Example1). In a specific embodiment, Cys-146 is replaced with a Serine aminoacid residue. Polypeptides encoding these polypeptides are alsoencompassed by the invention.

In another specific embodiment, Cys-232 of the Neutrokine-alpha sequenceshown in SEQ ID NO:2 is mutated to another amino acid residue, ordeleted altogether, for example, to aid preventing or diminishingoligomerization of the mutant Neutrokine-alpha polypeptide whenexpressed in a expression system (essentially as described in Example1). In a specific embodiment, Cys-232 is replaced with a Serine aminoacid residue. Polypeptides encoding these polypeptides are alsoencompassed by the invention.

In yet another specific embodiment, Cys-245 of the Neutrokine-alphasequence shown in SEQ ID NO:2 is mutated to another amino acid residue,or deleted altogether, for example, to aid preventing or diminishingoligomerization of the mutant Neutrokine-alpha polypeptide whenexpressed in a expression system (essentially as described in Example1). In a specific embodiment, Cys-245 is replaced with a Serine aminoacid residue. Polypeptides encoding these polypeptides are alsoencompassed by the invention.

The polypeptides of the present invention are preferably provided in anisolated form, and preferably are substantially purified. Arecombinantly produced version of the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides can be substantially purified by theone-step method described in Smith and Johnson, Gene 67:31-40 (1988).

The polypeptides of the present invention include the completepolypeptide encoded by the deposited cDNA (ATCC Deposit No. 97768)including the intracellular, transmembrane and extracellular domains ofthe polypeptide encoded by the deposited cDNA, the mature solublepolypeptide encoded by the deposited cDNA, the extracellular domainminus the intracellular and transmembrane domains of the protein, thecomplete polypeptide of FIGS. 1A and 1B (amino acid residues 1-285 ofSEQ ID NO:2), the mature soluble polypeptide of FIGS. 1A and 1B (aminoacids 134-285 of SEQ ID NO:2), the extracellular domain of FIGS. 1A and1B (amino acid residues 73-285 of SEQ ID NO:2) minus the intracellularand transmembrane domains, as well as polypeptides which have at least80%, 85%, 90% similarity, more preferably at least 95% similarity, andstill more preferably at least 96%, 97%, 98% or 99% similarity to thosedescribed above. Polynucleotides encoding these polypeptides are alsoencompassed by the invention.

The polypeptides of the present invention also include the completepolypeptide encoded by the deposited cDNA including the intracellular,transmembrane and extracellular domains of the polypeptide encoded bythe deposited cDNA (ATCC Deposit No. 203518), the mature solublepolypeptide encoded by the deposited cDNA, the extracellular domainminus the intracellular and transmembrane domains of the protein, thecomplete polypeptide of FIGS. 5A and 5B (amino acid residues 1-266 ofSEQ ID NO:19), the extracellular domain of FIGS. 5A and 5B (amino acidresidues 73-266 of SEQ ID NO:19) minus the intracellular andtransmembrane domains, as well as polypeptides which have at least 80%,85%, 90% similarity, more preferably at least 95% similarity, and stillmore preferably at least 96%, 97%, 98% or 99% similarity to thosedescribed above. Polynucleotides encoding these polypeptides are alsoencompassed by the invention.

Further polypeptides of the present invention include polypeptides atleast 80%, or at least 85% identical, more preferably at least 90% or95% identical, still more preferably at least 96%, 97%, 98% or 99%identical to the polypeptide encoded by the deposited cDNA (ATCC DepositNo. 97768) or to the polypeptide of FIGS. 1A and 1B (SEQ ID NO:2), andalso include portions of such polypeptides with at least 30 amino acidsand more preferably at least 50 amino acids. Polynucleotides encodingthese polypeptides are also encompassed by the invention.

Further polypeptides of the present invention include polypeptides atleast 80%, or at least 85% identical, more preferably at least 90% or95% identical, still more preferably at least 96%, 97%, 98% or 99%identical to the polypeptide encoded by the deposited cDNA (ATCC DepositNo. 203518) or to the polypeptide of FIGS. 5A and 5B (SEQ ID NO:19), andalso include portions of such polypeptides with at least 30 amino acidsand more preferably at least 50 amino acids. Polynucleotides encodingthese polypeptides are also encompassed by the invention.

By “% similarity” for two polypeptides is intended a similarity scoreproduced by comparing the amino acid sequences of the two polypeptidesusing the Bestfit program (Wisconsin Sequence Analysis Package, Version8 for Unix, Genetics Computer Group, University Research Park, 575Science Drive, Madison, Wis. 53711) and the default settings fordetermining similarity. Bestfit uses the local homology algorithm ofSmith and Waterman (Advances in Applied Mathematics 2:482-489, 1981) tofind the best segment of similarity between two sequences.

By a polypeptide having an amino acid sequence at least, for example,95% “identical” to a reference amino acid sequence of a Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide is intended that the amino acidsequence of the polypeptide is identical to the reference sequenceexcept that the polypeptide sequence may include up to five amino acidalterations per each 100 amino acids of the reference amino acid of theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide. In other words,to obtain a polypeptide having an amino acid sequence at least 95%identical to a reference amino acid sequence, up to 5% of the amino acidresidues in the reference sequence may be deleted or substituted withanother amino acid, or a number of amino acids up to 5% of the totalamino acid residues in the reference sequence may be inserted into thereference sequence. These alterations of the reference sequence mayoccur at the amino or carboxy terminal positions of the reference aminoacid sequence or anywhere between those terminal positions, interspersedeither individually among residues in the reference sequence or in oneor more contiguous groups within the reference sequence.

As a practical matter, whether any particular polypeptide is at least80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to, for instance, theamino acid sequence shown in FIGS. 1A and 1B (SEQ ID NO:2), the aminoacid sequence encoded by the deposited cDNA clone HNEDU15 (ATCCAccession No. 97768), or fragments thereof, or, for instance, to theamino acid sequence shown in FIGS. 5A and 5B (SEQ ID NO:19), the aminoacid sequence encoded by the deposited cDNA clone HDPMC52 (ATCCAccession No. 203518), or fragments thereof, can be determinedconventionally using known computer programs such the Bestfit program(Wisconsin Sequence Analysis Package, Version 8 for Unix, GeneticsComputer Group, University Research Park, 575 Science Drive, Madison,Wis. 53711). When using Bestfit or any other sequence alignment programto determine whether a particular sequence is, for instance, 95%identical to a reference sequence according to the present invention,the parameters are set, of course, such that the percentage of identityis calculated over the full length of the reference amino acid sequenceand that gaps in homology of up to 5% of the total number of amino acidresidues in the reference sequence are allowed.

In a specific embodiment, the identity between a reference (query)sequence (a sequence of the present invention) and a subject sequence,also referred to as a global sequence alignment, is determined using theFASTDB computer program based on the algorithm of Brutlag et al. (Comp.App. Biosci. 6:237-245 (1990)). Preferred parameters used in a FASTDBamino acid alignment are: Matrix=PAM 0, k-tuple=2, Mismatch Penalty=1,Joining Penalty=20, Randomization Group Length=0, Cutoff Score=1, WindowSize=sequence length, Gap Penalty=5, Gap Size Penalty=0.05, WindowSize=500 or the length of the subject amino acid sequence, whichever isshorter. According to this embodiment, if the subject sequence isshorter than the query sequence due to N- or C-terminal deletions, notbecause of internal deletions, a manual correction is made to theresults to take into consideration the fact that the FASTDB program doesnot account for N- and C-terminal truncations of the subject sequencewhen calculating global percent identity. For subject sequencestruncated at the N- and C-termini, relative to the query sequence, thepercent identity is corrected by calculating the number of residues ofthe query sequence that are N- and C-terminal of the subject sequence,which are not matched/aligned with a corresponding subject residue, as apercent of the total bases of the query sequence. A determination ofwhether a residue is matched/aligned is determined by results of theFASTDB sequence alignment. This percentage is then subtracted from thepercent identity, calculated by the above FASTDB program using thespecified parameters, to arrive at a final percent identity score. Thisfinal percent identity score is what is used for the purposes of thisembodiment. Only residues to the N- and C-termini of the subjectsequence, which are not matched/aligned with the query sequence, areconsidered for the purposes of manually adjusting the percent identityscore. That is, only query residue positions outside the farthest N- andC-terminal residues of the subject sequence. For example, a 90 aminoacid residue subject sequence is aligned with a 100 residue querysequence to determine percent identity. The deletion occurs at theN-terminus of the subject sequence and therefore, the FASTDB alignmentdoes not show a matching/alignment of the first 10 residues at theN-terminus. The 10 unpaired residues represent 10% of the sequence(number of residues at the N- and C-termini not matched/total number ofresidues in the query sequence) so 10% is subtracted from the percentidentity score calculated by the FASTDB program. If the remaining 90residues were perfectly matched the final percent identity would be 90%.In another example, a 90 residue subject sequence is compared with a 100residue query sequence. This time the deletions are internal deletionsso there are no residues at the N- or C-termini of the subject sequencewhich are not matched/aligned with the query. In this case the percentidentity calculated by FASTDB is not manually corrected. Once again,only residue positions outside the N- and C-terminal ends of the subjectsequence, as displayed in the FASTDB alignment, which are notmatched/aligned with the query sequence are manually corrected for. Noother manual corrections are made for the purposes of this embodiment.

The polypeptides of the present invention have uses that include, butare not limited to, as a molecular weight marker on SDS-PAGE gels or onmolecular sieve gel filtration columns using methods well known to thoseskilled in the art. Additionally, as described in detail below, thepolypeptides of the present invention have uses that include, but arenot limited to, to raise polyclonal and monoclonal antibodies, which areuseful in assays for detecting Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide expression as described below or asagonists and antagonists capable of enhancing or inhibitingNeutrokine-alpha and/or Neutrokine-alphaSV function. The polypeptides ofthe invention also have therapeutic uses as described herein. Further,such polypeptides can be used in the yeast two-hybrid system to“capture” Neutrokine-alpha and/or Neutrokine-alphaSV binding proteinswhich are also candidate agonists and antagonists according to thepresent invention. The yeast two hybrid system is described in Fieldsand Song, Nature 340:245-246 (1989).

Transgenics and “Knock-Outs”

The polypeptides of the invention can also be expressed in transgenicanimals. Animals of any species, including, but not limited to, mice,rats, rabbits, hamsters, guinea pigs, pigs, micro-pigs, goats, sheep,cows and non-human primates, e.g., baboons, monkeys, and chimpanzees maybe used to generate transgenic animals. In a specific embodiment,techniques described herein or otherwise known in the art, are used toexpress polypeptides of the invention in humans, as part of a genetherapy protocol.

Any technique known in the art may be used to introduce the transgene(i.e., polynucleotides of the invention) into animals to produce thefounder lines of transgenic animals. Such techniques include, but arenot limited to, pronuclear microinjection (Paterson, et al., Appl.Microbiol. Biotechnol. 40:691-698 (1994); Carver et al., Biotechnology(NY) 11:1263-1270 (1993); Wright et al., Biotechnology (NY) 9:830-834(1991); and Hoppe et al., U.S. Pat. No. 4,873,191 (1989)); retrovirusmediated gene transfer into germ lines (Van der Putten et al., Proc.Natl. Acad. Sci., USA 82:6148-6152 (1985)), blastocysts or embryos; genetargeting in embryonic stem cells (Thompson et al., Cell 56:313-321(1989)); electroporation of cells or embryos (Lo, 1983, Mol. Cell. Biol.3:1803-1814 (1983)); introduction of the polynucleotides of theinvention using a gene gun (see, e.g., Ulmer et al., Science 259:1745(1993); introducing nucleic acid constructs into embryonic pluripotentstem cells and transferring the stem cells back into the blastocyst; andsperm-mediated gene transfer (Lavitrano et al., Cell 57:717-723 (1989);etc. For a review of such techniques, see Gordon, “Transgenic Animals,”Intl. Rev. Cytol. 115:171-229 (1989), which is incorporated by referenceherein in its entirety. See also, U.S. Pat. No. 5,464,764 (Capecchi, etal., Positive-Negative Selection Methods and Vectors); U.S. Pat. No.5,631,153 (Capecchi, et al., Cells and Non-Human Organisms ContainingPredetermined Genomic Modifications and Positive-Negative SelectionMethods and Vectors for Making Same); U.S. Pat. No. 4,736,866 (Leder, etal., Transgenic Non-Human Animals); and U.S. Pat. No. 4,873,191 (Wagner,et al., Genetic Transformation of Zygotes); each of which is herebyincorporated by reference in its entirety.

Any technique known in the art may be used to produce transgenic clonescontaining polynucleotides of the invention, for example, nucleartransfer into enucleated oocytes of nuclei from cultured embryonic,fetal, or adult cells induced to quiescence (Campell et al., Nature380:64-66 (1996); Wilmut et al., Nature 385:810-813 (1997)).

The present invention provides for transgenic animals that carry thetransgene in all their cells, as well as animals which carry thetransgene in some, but not all their cells, i.e., mosaic or chimericanimals. The transgene may be integrated as a single transgene or asmultiple copies such as in concatamers, e.g., head-to-head tandems orhead-to-tail tandems. The transgene may also be selectively introducedinto and activated in a particular cell type by following, for example,the teaching of Lasko et al. (Lasko et al., Proc. Natl. Acad. Sci. USA89:6232-6236 (1992)). The regulatory sequences required for such acell-type specific activation will depend upon the particular cell typeof interest, and will be apparent to those of skill in the art. When itis desired that the polynucleotide transgene be integrated into thechromosomal site of the endogenous gene, gene targeting is preferred.Briefly, when such a technique is to be utilized, vectors containingsome nucleotide sequences homologous to the endogenous gene are designedfor the purpose of integrating, via homologous recombination withchromosomal sequences, into and disrupting the function of thenucleotide sequence of the endogenous gene. The transgene may also beselectively introduced into a particular cell type, thus inactivatingthe endogenous gene in only that cell type, by following, for example,the teaching of Gu et al. (Gu et al., Science 265:103-106 (1994)). Theregulatory sequences required for such a cell-type specific inactivationwill depend upon the particular cell type of interest, and will beapparent to those of skill in the art. In addition to expressing thepolypeptide of the present invention in a ubiquitous or tissue specificmanner in transgenic animals, it would also be routine for one skilledin the art to generate constructs which regulate expression of thepolypeptide by a variety of other means (for example, developmentally orchemically regulated expression).

Once transgenic animals have been generated, the expression of therecombinant gene may be assayed utilizing standard techniques. Initialscreening may be accomplished by Southern blot analysis or PCRtechniques to analyze animal tissues to verify that integration of thetransgene has taken place. The level of mRNA expression of the transgenein the tissues of the transgenic animals may also be assessed usingtechniques which include, but are not limited to, Northern blot analysisof tissue samples obtained from the animal, in situ hybridizationanalysis, reverse transcriptase-PCR (rt-PCR); and TaqMan PCR. Samples oftransgenic gene-expressing tissue may also be evaluatedimmunocytochemically or immunohistochemically using antibodies specificfor the transgene product.

Once the founder animals are produced, they may be bred, inbred,outbred, or crossbred to produce colonies of the particular animal.Examples of such breeding strategies include, but are not limited to:outbreeding of founder animals with more than one integration site inorder to establish separate lines; inbreeding of separate lines in orderto produce compound transgenics that express the transgene at higherlevels because of the effects of additive expression of each transgene;crossing of heterozygous transgenic animals to produce animalshomozygous for a given integration site in order to both augmentexpression and eliminate the need for screening of animals by DNAanalysis; crossing of separate homozygous lines to produce compoundheterozygous or homozygous lines; breeding to place the transgene on adistinct background that is appropriate for an experimental model ofinterest; and breeding of transgenic animals to other animals bearing adistinct transgene or knockout mutation.

Transgenic and “knock-out” animals of the invention have uses whichinclude, but are not limited to, animal model systems useful inelaborating the biological function of Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides, studying conditions and/or disordersassociated with aberrant Neutrokine-alpha and/or Neutrokine-alphaSVexpression, and in screening for compounds effective in amelioratingsuch conditions and/or disorders.

In further embodiments of the invention, cells that are geneticallyengineered to express the polypeptides of the invention, oralternatively, that are genetically engineered not to express thepolypeptides of the invention (e.g., knockouts) are administered to apatient in vivo. Such cells may be obtained from the patient (i.e.,animal, including human) or an MHC compatible donor and can include, butare not limited to fibroblasts, bone marrow cells, blood cells (e.g.,lymphocytes), adipocytes, muscle cells, endothelial cells etc. The cellsare genetically engineered in vitro using recombinant DNA techniques tointroduce the coding sequence of polypeptides of the invention into thecells, or alternatively, to disrupt the coding sequence and/orendogenous regulatory sequence associated with the polypeptides of theinvention, e.g., by transduction (using viral vectors, and preferablyvectors that integrate the transgene into the cell genome) ortransfection procedures, including, but not limited to, the use ofplasmids, cosmids, YACs, naked DNA, electroporation, liposomes, etc. Thecoding sequence of the polypeptides of the invention can be placed underthe control of a strong constitutive or inducible promoter orpromoter/enhancer to achieve expression, and preferably secretion, ofthe polypeptides of the invention. The engineered cells which expressand preferably secrete the polypeptides of the invention can beintroduced into the patient systemically, e.g., in the circulation, orintraperitoneally.

Alternatively, the cells can be incorporated into a matrix and implantedin the body, e.g., genetically engineered fibroblasts can be implantedas part of a skin graft; genetically engineered endothelial cells can beimplanted as part of a lymphatic or vascular graft. (See, for example,Anderson et al. U.S. Pat. No. 5,399,349; and Mulligan & Wilson, U.S.Pat. No. 5,460,959 each of which is incorporated by reference herein inits entirety).

When the cells to be administered are non-autologous or non-MHCcompatible cells, they can be administered using well known techniqueswhich prevent the development of a host immune response against theintroduced cells. For example, the cells may be introduced in anencapsulated form which, while allowing for an exchange of componentswith the immediate extracellular environment, does not allow theintroduced cells to be recognized by the host immune system.

Antibodies

Further polypeptides of the invention relate to antibodies and T-cellantigen receptors (TCR) which immunospecifically bind a polypeptide,polypeptide fragment, or variant of SEQ ID NO:2 and/or SEQ ID NO:19,and/or an epitope, of the present invention (as determined byimmunoassays well known in the art for assaying specificantibody-antigen binding). Antibodies of the invention include, but arenot limited to, polyclonal, monoclonal, multispecific, human, humanizedor chimeric antibodies, single chain antibodies, Fab fragments, F(ab′)fragments, fragments produced by a Fab expression library,anti-idiotypic (anti-Id) antibodies (including, e.g., anti-id antibodiesto antibodies of the invention), and epitope-binding fragments of any ofthe above. The term “antibody,” as used herein, refers to immunoglobulinmolecules and immunologically active portions of immunoglobulinmolecules, i.e., molecules that contain an antigen binding site thatimmunospecifically binds an antigen. The immunoglobulin molecules of theinvention can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY),class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass ofimmunoglobulin molecule. Immunoglobulins may have both a heavy and lightchain. An array of IgG, IgE, IgM, IgD, IgA, and IgY heavy chains may bepaired with a light chain of the kappa or lambda forms.

Most preferably the antibodies are human antigen-binding antibodyfragments of the present invention and include, but are not limited to,Fab, Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chainantibodies, disulfide-linked Fvs (sdFv) and fragments comprising eithera VL or VH domain. Antigen-binding antibody fragments, includingsingle-chain antibodies, may comprise the variable region(s) alone or incombination with the entirety or a portion of the following: hingeregion, CH1, CH2, and CH3 domains. Also included in the invention areantigen-binding fragments also comprising any combination of variableregion(s) with a hinge region, CH1, CH2, and CH3 domains. The antibodiesof the invention may be from any animal origin including birds andmammals. Preferably, the antibodies are human, murine (e.g., mouse andrat), donkey, ship rabbit, goat, guinea pig, camel, horse, or chicken.As used herein, “human” antibodies include antibodies having the aminoacid sequence of a human immunoglobulin and include antibodies isolatedfrom human immunoglobulin libraries or from animals transgenic for oneor more human immunoglobulin and that do not express endogenousimmunoglobulins, as described infra and, for example in, U.S. Pat. No.5,939,598 by Kucherlapati et al.

The antibodies of the present invention may be monospecific, bispecific,trispecific or of greater multispecificity. Multispecific antibodies maybe specific for different epitopes of a polypeptide of the presentinvention or may be specific for both a polypeptide of the presentinvention as well as for a heterologous epitope, such as a heterologouspolypeptide or solid support material. See, e.g., PCT publications WO93/17715; WO 92/08802; WO91/00360; WO 92/05793; Tutt, et al., J.Immunol. 147:60-69 (1991); U.S. Pat. Nos. 4,474,893; 4,714,681;4,925,648; 5,573,920; 5,601,819; Kostelny et al., J. Immunol.148:1547-1553 (1992).

Antibodies of the present invention may be described or specified interms of the epitope(s) or portion(s) of a polypeptide of the presentinvention which they recognize or specifically bind. The epitope(s) orpolypeptide portion(s) may be specified as described herein, e.g., byN-terminal and C-terminal positions, by size in contiguous amino acidresidues, or listed in the Tables and Figures. Antibodies whichspecifically bind any epitope or polypeptide of the present inventionmay also be excluded. Therefore, the present invention includesantibodies that specifically bind polypeptides of the present invention,and allows for the exclusion of the same.

In specific embodiments, antibodies of the invention bind topolypeptides comprising Phe-115 to Leu-147, Ile-150 to Tyr-163, Ser-171to Phe-194, Glu-223 to Tyr-246, and Ser-271 to Phe-278 of the amino acidsequence of SEQ ID NO:2. In another specific embodiment, antibodies ofthe invention bind to polypeptides consisting of Phe-115 to Leu-147,Ile-150 to Tyr-163, Ser-171 to Phe-194, Glu-223 to Tyr-246, and Ser-271to Phe-278 of the amino acid sequence of SEQ ID NO:2. In a preferredembodiment, antibodies of the invention bind to a polypeptide comprisingGlu-223 to Tyr-246 of SEQ ID NO:2. In another preferred embodiment,antibodies of the invention bind to a polypeptide consisting of Glu-223to Tyr-246 of SEQ ID NO:2. In a more preferred embodiment, antibodies ofthe invention bind to a polypeptide consisting of Phe-230 to Asn-242 ofSEQ ID NO:2. In further preferred, nonexclusive embodiments, theantibodies of the invention inhibit one or more biological activities ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides of the inventionthrough specific binding. In more preferred embodiments, the antibody ofthe invention inhibits Neutrokine-alpha- and/orNeutrokine-alphaSV-mediated B cell proliferation.

Antibodies of the present invention may also be described or specifiedin terms of their cross-reactivity. Antibodies that do not bind anyother analog, ortholog, or homolog of a polypeptide of the presentinvention are included. Antibodies that bind polypeptides with at least95%, at least 90%, at least 85%, at least 80%, at least 75%, at least70%, at least 65%, at least 60%, at least 55%, and at least 50% identity(as calculated using methods known in the art and described herein) to apolypeptide of the present invention are also included in the presentinvention. In specific embodiments, antibodies of the present inventioncross-react with murine, rat and/or rabbit homologs of human proteinsand the corresponding epitopes thereof. Antibodies that do not bindpolypeptides with less than 95%, less than 90%, less than 85%, less than80%, less than 75%, less than 70%, less than 65%, less than 60%, lessthan 55%, and less than 50% identity (as calculated using methods knownin the art and described herein) to a polypeptide of the presentinvention are also included in the present invention. In a specificembodiment, the above-described cross-reactivity is with respect to anysingle specific antigenic or immunogenic polypeptide, or combination(s)of 2, 3, 4, 5, or more of the specific antigenic and/or immunogenicpolypeptides disclosed herein. Further included in the present inventionare antibodies which bind polypeptides encoded by polynucleotides whichhybridize to a polynucleotide of the present invention underhybridization conditions (as described herein). Antibodies of thepresent invention may also be described or specified in terms of theirbinding affinity to a polypeptide of the invention. Preferred bindingaffinities include those with a dissociation constant or Kd less than5×10⁻⁵ M, 10⁻⁵ M, 5×10⁻⁶ M, 10⁻⁶M, 5×10⁻⁷M, 10⁷ M, 5×10⁻⁸M, 10⁻⁸M,5×10⁻⁹ M, 10⁻⁹ M, 5×10⁻¹⁰ M, 10⁻¹⁰ M, 5×10⁻¹¹ M, 10⁻¹¹ M, 5×10⁻¹² M,10⁻¹² M, 5×10⁻¹³ M, 10⁻¹³ M, 5×10⁻¹⁴ M, 10⁻¹⁴ M, 5×10⁻¹⁵ M, 10⁻¹⁵ M.

The invention also provides antibodies that competitively inhibitbinding of an antibody to an epitope of the invention as determined byany method known in the art for determining competitive binding, forexample, the immunoassays described herein. In preferred embodiments,the antibody competitively inhibits binding to the epitope by at least95%, at least 90%, at least 85%, at least 80%, at least 75%, at least70%, at least 60%, or at least 50%.

Antibodies of the present invention may act as agonists or antagonistsof the polypeptides of the present invention. For example, the presentinvention includes antibodies which disrupt the receptor/ligandinteractions with the polypeptides of the invention either partially orfully. Preferably, antibodies of the present invention bind an antigenicepitope disclosed herein, or a portion thereof. The invention featuresboth receptor-specific antibodies and ligand-specific antibodies. Theinvention also features receptor-specific antibodies which do notprevent ligand binding but prevent receptor activation. Receptoractivation (i.e., signaling) may be determined by techniques describedherein or otherwise known in the art. For example, receptor activationcan be determined by detecting the phosphorylation (e.g., tyrosine orserine/threonine) of the receptor or its substrate byimmunoprecipitation followed by western blot analysis (for example, asdescribed supra). In specific embodiments, antibodies are provided thatinhibit ligand activity or receptor activity by at least 95%, at least90%, at least 85%, at least 80%, at least 75%, at least 70%, at least60%, or at least 50% of the activity in absence of the antibody.

The invention also features receptor-specific antibodies which bothprevent ligand binding and receptor activation as well as antibodiesthat recognize the receptor-ligand complex, and, preferably, do notspecifically recognize the unbound receptor or the unbound ligand.Likewise, included in the invention are neutralizing antibodies whichbind the ligand and prevent binding of the ligand to the receptor, aswell as antibodies which bind the ligand, thereby preventing receptoractivation, but do not prevent the ligand from binding the receptor.Further included in the invention are antibodies which activate thereceptor. These antibodies may act as receptor agonists, i.e.,potentiate or activate either all or a subset of the biologicalactivities of the ligand-mediated receptor activation, for example, byinducing dimerization of the receptor. The antibodies may be specifiedas agonists, antagonists or inverse agonists for biological activitiescomprising the specific biological activities of the peptides of theinvention disclosed herein. The above antibody agonists can be madeusing methods known in the art. See, e.g., PCT publication WO 96/40281;U.S. Pat. No. 5,811,097; Deng et al., Blood 92(6):1981-1988 (1998); Chenet al., Cancer Res. 58(16):3668-3678 (1998); Harrop et al., J. Immunol.161(4):1786-1794 (1998); Zhu et al., Cancer Res. 58(15):3209-3214(1998); Yoon et al., J. Immunol. 160(7):3170-3179 (1998); Prat et al.,J. Cell. Sci. 111(Pt2):237-247 (1998); Pitard et al., J. Immunol.Methods 205(2):177-190 (1997); Liautard et al., Cytokine 9(4):233-241(1997); Carlson et al., J. Biol. Chem. 272(17):11295-11301 (1997);Taryman et al., Neuron 14(4):755-762 (1995); Muller et al., Structure6(9):1153-1167 (1998); Bartunek et al., Cytokine 8(1):14-20 (1996)(which are all incorporated by reference herein in their entireties).

Antibodies of the present invention may be used, for example, but notlimited to, to purify, detect, and target the polypeptides of thepresent invention, including both in vitro and in vivo diagnostic andtherapeutic methods. For example, the antibodies have use inimmunoassays for qualitatively and quantitatively measuring levels ofthe polypeptides of the present invention in biological samples. See,e.g., Harlow et al., Antibodies: A Laboratory Manual, (Cold SpringHarbor Laboratory Press, 2nd ed. 1988) (incorporated by reference hereinin its entirety).

As discussed in more detail below, the antibodies of the presentinvention may be used either alone or in combination with othercompositions. The antibodies may further be recombinantly fused to aheterologous polypeptide at the N- or C-terminus or chemicallyconjugated (including covalent and non-covalent conjugations) topolypeptides or other compositions. For example, antibodies of thepresent invention may be recombinantly fused or conjugated to moleculesuseful as labels in detection assays and effector molecules such asheterologous polypeptides, drugs, radionuclides, or toxins. See, e.g.,PCT publications WO 92/08495; WO 91/14438; WO 89/12624; U.S. Pat. No.5,314,995; and EP 396,387.

The antibodies of the invention include derivatives that are modified,i.e., by the covalent attachment of any type of molecule to the antibodysuch that covalent attachment does not prevent the antibody fromgenerating an anti-idiotypic response. For example, but not by way oflimitation, the antibody derivatives include antibodies that have beenmodified, e.g., by glycosylation, acetylation, pegylation,phosphorylation, amidation, derivatization by known protecting/blockinggroups, proteolytic cleavage, linkage to a cellular ligand or otherprotein, etc. Any of numerous chemical modifications may be carried outby known techniques, including, but not limited to specific chemicalcleavage, acetylation, formylation, metabolic synthesis of tunicamycin,etc. Additionally, the derivative may contain one or more non-classicalamino acids.

The antibodies of the present invention may be generated by any suitablemethod known in the art. Polyclonal antibodies to an antigen-of-interestcan be produced by various procedures well known in the art. Forexample, a polypeptide of the invention can be administered to varioushost animals including, but not limited to, rabbits, mice, rats, etc. toinduce the production of sera containing polyclonal antibodies specificfor the antigen. Various adjuvants may be used to increase theimmunological response, depending on the host species, and include butare not limited to, Freund's (complete and incomplete), mineral gelssuch as aluminum hydroxide, surface active substances such aslysolecithin, pluronic polyols, polyanions, peptides, oil emulsions,keyhole limpet hemocyanins, dinitrophenol, and potentially useful humanadjuvants such as BCG (bacille Calmette-Guerin) and corynebacteriumparvum. Such adjuvants are also well known in the art.

Monoclonal antibodies can be prepared using a wide variety of techniquesknown in the art including the use of hybridoma, recombinant, and phagedisplay technologies, or a combination thereof. For example, monoclonalantibodies can be produced using hybridoma techniques including thoseknown in the art and taught, for example, in Harlow et al., Antibodies:A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed.1988); Hammerling, et al., in: Monoclonal Antibodies and T-CellHybridomas 563-681 (Elsevier, N.Y., 1981) (said references incorporatedby reference in their entireties). The term “monoclonal antibody” asused herein is not limited to antibodies produced through hybridomatechnology. The term “monoclonal antibody” refers to an antibody that isderived from a single clone, including any eukaryotic, prokaryotic, orphage clone, and not the method by which it is produced.

A “monoclonal antibody” may comprise, or alternatively consist of, twoproteins, i.e., a heavy and a light chain.

Methods for producing and screening for specific antibodies usinghybridoma technology are routine and well known in the art and arediscussed in detail in the Examples (e.g., Example 9). In a non-limitingexample, mice can be immunized with a polypeptide of the invention or acell expressing such peptide. Once an immune response is detected, e.g.,antibodies specific for the antigen are detected in the mouse serum, themouse spleen is harvested and splenocytes isolated. The splenocytes arethen fused by well-known techniques to any suitable myeloma cells, forexample cells from cell line SP20 available from the ATCC. Hybridomasare selected and cloned by limited dilution. The hybridoma clones arethen assayed by methods known in the art for cells that secreteantibodies capable of binding a polypeptide of the invention. Ascitesfluid, which generally contains high levels of antibodies, can begenerated by immunizing mice with positive hybridoma clones.

Accordingly, the present invention provides methods of generatingmonoclonal antibodies as well as antibodies produced by the methodcomprising culturing a hybridoma cell secreting an antibody of theinvention wherein, preferably, the hybridoma is generated by fusingsplenocytes isolated from a mouse immunized with an antigen of theinvention with myeloma cells and then screening the hybridomas resultingfrom the fusion for hybridoma clones that secrete an antibody able tobind a polypeptide of the invention.

Antibody fragments which recognize specific epitopes may be generated byknown techniques. For example, Fab and F(ab′)2 fragments of theinvention may be produced by proteolytic cleavage of immunoglobulinmolecules, using enzymes such as papain (to produce Fab fragments) orpepsin (to produce F(ab′)2 fragments). F(ab′)2 fragments contain thevariable region, the light chain constant region and the CH1 domain ofthe heavy chain.

For example, the antibodies of the present invention can also begenerated using various phage display methods known in the art. In phagedisplay methods, functional antibody domains are displayed on thesurface of phage particles which carry the polynucleotide sequencesencoding them. In a particular embodiment, such phage can be utilized todisplay antigen-binding domains expressed from a repertoire orcombinatorial antibody library (e.g., human or murine). Phage expressingan antigen binding domain that binds the antigen of interest can beselected or identified with antigen, e.g., using labeled antigen orantigen bound or captured to a solid surface or bead. Phage used inthese methods are typically filamentous phage including fd and M13binding domains expressed from phage with Fab, Fv or disulfidestabilized Fv antibody domains recombinantly fused to either the phagegene III or gene VIII protein. Examples of phage display methods thatcan be used to make the antibodies of the present invention includethose disclosed in Brinkman et al., J. Immunol. Methods 182:41-50(1995); Ames et al., J. Immunol. Methods 184:177-186 (1995);Kettleborough et al., Eur. J. Immunol. 24:952-958 (1994); Persic et al.,Gene 187 9-18 (1997); Burton et al., Advances in Immunology 57:191-280(1994); PCT application No. PCT/GB91/01134; PCT publications WO90/02809; WO 91/10737; WO 92/01047; WO 92/18619; WO 93/11236; WO95/15982; WO 95/20401; and U.S. Pat. Nos. 5,698,426; 5,223,409;5,403,484; 5,580,717; 5,427,908; 5,750,753; 5,821,047; 5,571,698;5,427,908; 5,516,637; 5,780,225; 5,658,727; 5,733,743 and 5,969,108;each of which is incorporated herein by reference in its entirety.

As described in the above references, after phage selection, theantibody coding regions from the phage can be isolated and used togenerate whole antibodies, including human antibodies, or any otherdesired antigen binding fragment, and expressed in any desired host,including mammalian cells, insect cells, plant cells, yeast, andbacteria, e.g., as described in detail below. For example, techniques torecombinantly produce Fab, Fab′ and F(ab′)2 fragments can also beemployed using methods known in the art such as those disclosed in PCTpublication WO 92/22324; Mullinax et al., BioTechniques 12(6):864-869(1992); and Sawai et al., AJRI 34:26-34 (1995); and Better et al.,Science 240:1041-1043 (1988) (said references incorporated by referencein their entireties).

Examples of techniques which can be used to produce single-chain Fvs andantibodies include those described in U.S. Pat. Nos. 4,946,778 and5,258,498; Huston et al., Methods in Enzymology 203:46-88 (1991); Shu etal., PNAS 90:7995-7999 (1993); and Skerra et al., Science 240:1038-1040(1988). For some uses, including in vivo use of antibodies in humans andin vitro detection assays, it may be preferable to use chimeric,humanized, or human antibodies. A chimeric antibody is a molecule inwhich different portions of the antibody are derived from differentanimal species, such as antibodies having a variable region derived froma murine monoclonal antibody and a human immunoglobulin constant region.Methods for producing chimeric antibodies are known in the art. Seee.g., Morrison, Science 229:1202 (1985); Oi et al., BioTechniques 4:214(1986); Gillies et al., (1989) J. Immunol. Methods 125:191-202; U.S.Pat. Nos. 5,807,715; 4,816,567; and 4,816,397, which are incorporatedherein by reference in their entirety. Humanized antibodies are antibodymolecules from non-human species antibody that bind the desired antigenhaving one or more complementarity determining regions (CDRs) from thenon-human species and a framework region from a human immunoglobulinmolecule. Often, framework residues in the human framework regions willbe substituted with the corresponding residue from the CDR donorantibody to alter, preferably improve, antigen binding. These frameworksubstitutions are identified by methods well known in the art, e.g., bymodeling of the interactions of the CDR and framework residues toidentify framework residues important for antigen binding and sequencecomparison to identify unusual framework residues at particularpositions. (See, e.g., Queen et al., U.S. Pat. No. 5,585,089; Riechmannet al., Nature 332:323 (1988), which are incorporated herein byreference in their entireties.) Antibodies can be humanized using avariety of techniques known in the art including, for example,CDR-grafting (EP 239,400; PCT publication WO 91/09967; U.S. Pat. Nos.5,225,539; 5,530,101; and 5,585,089), veneering or resurfacing (EP592,106; EP 519,596; Padlan, Molecular Immunology 28(4/5):489-498(1991); Studnicka et al., Protein Engineering 7(6):805-814 (1994);Roguska. et al., PNAS 91:969-973 (1994)), and chain shuffling (U.S. Pat.No. 5,565,332).

Completely human antibodies are particularly desirable for therapeutictreatment of human patients. Human antibodies can be made by a varietyof methods known in the art including phage display methods describedabove using antibody libraries derived from human immunoglobulinsequences. See also, U.S. Pat. Nos. 4,444,887 and 4,716,111; and PCTpublications WO 98/46645, WO 98/50433, WO 98/24893, WO 98/16654, WO96/34096, WO 96/33735, and WO 91/10741; each of which is incorporatedherein by reference in its entirety.

Human antibodies can also be produced using transgenic mice which areincapable of expressing functional endogenous immunoglobulins, but whichcan express human immunoglobulin genes. For example, the human heavy andlight chain immunoglobulin gene complexes may be introduced randomly orby homologous recombination into mouse embryonic stem cells.Alternatively, the human variable region, constant region, and diversityregion may be introduced into mouse embryonic stem cells in addition tothe human heavy and light chain genes. The mouse heavy and light chainimmunoglobulin genes may be rendered non-functional separately orsimultaneously with the introduction of human immunoglobulin loci byhomologous recombination. In particular, homozygous deletion of the JHregion prevents endogenous antibody production. The modified embryonicstem cells are expanded and microinjected into blastocysts to producechimeric mice. The chimeric mice are then bred to produce homozygousoffspring which express human antibodies. The transgenic mice areimmunized in the normal fashion with a selected antigen, e.g., all or aportion of a polypeptide of the invention. Monoclonal antibodiesdirected against the antigen can be obtained from the immunized,transgenic mice using conventional hybridoma technology. The humanimmunoglobulin transgenes harbored by the transgenic mice rearrangeduring B cell differentiation, and subsequently undergo class switchingand somatic mutation. Thus, using such a technique, it is possible toproduce therapeutically useful IgG, IgA, IgM and IgE antibodies. For anoverview of this technology for producing human antibodies, see Lonbergand Huszar, Int. Rev. Immunol. 13:65-93 (1995). For a detaileddiscussion of this technology for producing human antibodies and humanmonoclonal antibodies and protocols for producing such antibodies, see,e.g., PCT publications WO 98/24893; WO 92/01047; WO 96/34096; WO96/33735; European Patent No. 0 598 877; U.S. Pat. Nos. 5,413,923;5,625,126; 5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318;5,885,793; 5,916,771; and 5,939,598, which are incorporated by referenceherein in their entirety. In addition, companies such as Abgenix, Inc.(Freemont, Calif.) and Genpharm (San Jose, Calif.) can be engaged toprovide human antibodies directed against a selected antigen usingtechnology similar to that described above.

Completely human antibodies which recognize a selected epitope can begenerated using a technique referred to as “guided selection.” In thisapproach a selected non-human monoclonal antibody, e.g., a mouseantibody, is used to guide the selection of a completely human antibodyrecognizing the same epitope. (Jespers et al., Bio/technology 12:899-903(1988)).

Further, antibodies to the polypeptides of the invention can, in turn,be utilized to generate anti-idiotype antibodies that “mimic”polypeptides of the invention using techniques well known to thoseskilled in the art. (See, e.g., Greenspan & Bona, FASEB J. 7(5):437-444;(1989) and Nissinoff, J. Immunol. 147(8):2429-2438 (1991)). For example,antibodies which bind to and competitively inhibit polypeptidemultimerization and/or binding of a polypeptide of the invention to aligand can be used to generate anti-idiotypes that “mimic” thepolypeptide multimerization and/or binding domain and, as a consequence,bind to and neutralize polypeptide and/or its ligand. Such neutralizinganti-idiotypes or Fab fragments of such anti-idiotypes can be used intherapeutic regimens to neutralize polypeptide ligand. For example, suchanti-idiotypic antibodies can be used to bind a polypeptide of theinvention and/or to bind its ligands/receptors, and thereby block itsbiological activity.

Polynucleotides Encoding Antibodies

The invention further provides polynucleotides comprising a nucleotidesequence encoding an antibody of the invention and fragments thereof.The invention also encompasses polynucleotides that hybridize understringent or lower stringency hybridization conditions, e.g., as definedsupra, to polynucleotides that encode an antibody, preferably, thatspecifically binds to a polypeptide of the invention, preferably, anantibody that binds to a polypeptide having the amino acid sequence ofSEQ ID NO:2. In another preferred embodiment, the antibody bindsspecifically to a polypeptide having the amino acid sequence of SEQ IDNO:19. In another preferred embodiment, the antibody binds specificallyto a polypeptide having the amino acid sequence of SEQ ID NO:23. Inanother preferred embodiment, the antibody binds specifically to apolypeptide having the amino acid sequence of SEQ ID NO:28. In anotherpreferred embodiment, the antibody binds specifically to a polypeptidehaving the amino acid sequence of SEQ ID NO:30.

The polynucleotides may be obtained, and the nucleotide sequence of thepolynucleotides determined, by any method known in the art. For example,if the nucleotide sequence of the antibody is known, a polynucleotideencoding the antibody may be assembled from chemically synthesizedoligonucleotides (e.g., as described in Kutmeier et al., BioTechniques17:242 (1994)), which, briefly, involves the synthesis of overlappingoligonucleotides containing portions of the sequence encoding theantibody, annealing and ligating of those oligonucleotides, and thenamplification of the ligated oligonucleotides by PCR.

Alternatively, a polynucleotide encoding an antibody may be generatedfrom nucleic acid from a suitable source. If a clone containing anucleic acid encoding a particular antibody is not available, but thesequence of the antibody molecule is known, a nucleic acid encoding theimmunoglobulin may be chemically synthesized or obtained from a suitablesource (e.g., an antibody cDNA library, or a cDNA library generatedfrom, or nucleic acid, preferably poly A+ RNA, isolated from, any tissueor cells expressing the antibody, such as hybridoma cells selected toexpress an antibody of the invention) by PCR amplification usingsynthetic primers hybridizable to the 3′ and 5′ ends of the sequence orby cloning using an oligonucleotide probe specific for the particulargene sequence to identify, e.g., a cDNA clone from a cDNA library thatencodes the antibody. Amplified nucleic acids generated by PCR may thenbe cloned into replicable cloning vectors using any method well known inthe art.

Once the nucleotide sequence and corresponding amino acid sequence ofthe antibody is determined, the nucleotide sequence of the antibody maybe manipulated using methods well known in the art for the manipulationof nucleotide sequences, e.g., recombinant DNA techniques, site directedmutagenesis, PCR, etc. (see, for example, the techniques described inSambrook et al., 1990, Molecular Cloning, A Laboratory Manual, 2d Ed.,Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. and Ausubel etal., eds., 1998, Current Protocols in Molecular Biology, John Wiley &Sons, NY, which are both incorporated by reference herein in theirentireties), to generate antibodies having a different amino acidsequence, for example to create amino acid substitutions, deletions,and/or insertions.

In a specific embodiment, the amino acid sequence of the heavy and/orlight chain variable domains may be inspected to identify the sequencesof the complementarity determining regions (CDRs) by methods that arewell known in the art, e.g., by comparison to known amino acid sequencesof other heavy and light chain variable regions to determine the regionsof sequence hypervariability. Using routine recombinant DNA techniques,one or more of the CDRs may be inserted within framework regions, e.g.,into human framework regions to humanize a non-human antibody, asdescribed supra. The framework regions may be naturally occurring orconsensus framework regions, and preferably human framework regions(see, e.g., Chothia et al., J. Mol. Biol. 278: 457-479 (1998) for alisting of human framework regions). Preferably, the polynucleotidegenerated by the combination of the framework regions and CDRs encodesan antibody that specifically binds a polypeptide of the invention.Preferably, as discussed supra, one or more amino acid substitutions maybe made within the framework regions, and, preferably, the amino acidsubstitutions improve binding of the antibody to its antigen.Additionally, such methods may be used to make amino acid substitutionsor deletions of one or more variable region cysteine residuesparticipating in an intrachain disulfide bond to generate antibodymolecules lacking one or more intrachain disulfide bonds. Otheralterations to the polynucleotide are encompassed by the presentinvention and within the skill of the art.

In addition, techniques developed for the production of “chimericantibodies” (Morrison et al., Proc. Natl. Acad. Sci. 81:851-855 (1984);Neuberger et al., Nature 312:604-608 (1984); Takeda et al., Nature314:452-454 (1985)) by splicing genes from a mouse antibody molecule ofappropriate antigen specificity together with genes from a humanantibody molecule of appropriate biological activity can be used. Asdescribed supra, a chimeric antibody is a molecule in which differentportions are derived from different animal species, such as those havinga variable region derived from a murine mAb and a human immunoglobulinconstant region, e.g., humanized antibodies.

Alternatively, techniques described for the production of single chainantibodies (U.S. Pat. No. 4,946,778; Bird, Science 242:423-42 (1988);Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883 (1988); and Wardet al., Nature 334:544-54 (1989)) can be adapted to produce single chainantibodies. Single chain antibodies are formed by linking the heavy andlight chain fragments of the Fv region via an amino acid bridge,resulting in a single chain polypeptide. Techniques for the assembly offunctional Fv fragments in E. coli may also be used (Skerra et al.,Science 242:1038-1041 (1988)).

Methods of Producing Antibodies

The antibodies of the invention can be produced by any method known inthe art for the synthesis of antibodies, in particular, by chemicalsynthesis or preferably, by recombinant expression techniques.

Recombinant expression of an antibody of the invention, or fragment,derivative or analog thereof, (e.g., a heavy or light chain of anantibody of the invention or a single chain antibody of the invention),requires construction of an expression vector containing apolynucleotide that encodes the antibody. Once a polynucleotide encodingan antibody molecule or a heavy or light chain of an antibody, orportion thereof (preferably containing the heavy or light chain variabledomain), of the invention has been obtained, the vector for theproduction of the antibody molecule may be produced by recombinant DNAtechnology using techniques well known in the art. Thus, methods forpreparing a protein by expressing a polynucleotide containing anantibody encoding nucleotide sequence are described herein. Methodswhich are well known to those skilled in the art can be used toconstruct expression vectors containing antibody coding sequences andappropriate transcriptional and translational control signals. Thesemethods include, for example, in vitro recombinant DNA techniques,synthetic techniques, and in vivo genetic recombination. The invention,thus, provides replicable vectors comprising a nucleotide sequenceencoding an antibody molecule of the invention, or a heavy or lightchain thereof, or a heavy or light chain variable domain, operablylinked to a promoter. Such vectors may include the nucleotide sequenceencoding the constant region of the antibody molecule (see, e.g., PCTPublication WO 86/05807; PCT Publication WO 89/01036; and U.S. Pat. No.5,122,464) and the variable domain of the antibody may be cloned intosuch a vector for expression of the entire heavy or light chain.

The expression vector is transferred to a host cell by conventionaltechniques and the transfected cells are then cultured by conventionaltechniques to produce an antibody of the invention. Thus, the inventionincludes host cells containing a polynucleotide encoding an antibody ofthe invention, or a heavy or light chain thereof, or a single chainantibody of the invention, operably linked to a heterologous promoter.In preferred embodiments for the expression of double-chainedantibodies, vectors encoding both the heavy and light chains may beco-expressed in the host cell for expression of the entireimmunoglobulin molecule, as detailed below.

A variety of host-expression vector systems may be utilized to expressthe antibody molecules of the invention. Such host-expression systemsrepresent vehicles by which the coding sequences of interest may beproduced and subsequently purified, but also represent cells which may,when transformed or transfected with the appropriate nucleotide codingsequences, express an antibody molecule of the invention in situ. Theseinclude but are not limited to microorganisms such as bacteria (e.g., E.coli, B. subtilis) transformed with recombinant bacteriophage DNA,plasmid DNA or cosmid DNA expression vectors containing antibody codingsequences; yeast (e.g., Saccharomyces, Pichia) transformed withrecombinant yeast expression vectors containing antibody codingsequences; insect cell systems infected with recombinant virusexpression vectors (e.g., baculovirus) containing antibody codingsequences; plant cell systems infected with recombinant virus expressionvectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus,TMV) or transformed with recombinant plasmid expression vectors (e.g.,Ti plasmid) containing antibody coding sequences; or mammalian cellsystems (e.g., COS, CHO, BHK, 293, 3T3 cells) harboring recombinantexpression constructs containing promoters derived from the genome ofmammalian cells (e.g., metallothionein promoter) or from mammalianviruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5Kpromoter). Preferably, bacterial cells such as Escherichia coli, andmore preferably, eukaryotic cells, especially for the expression ofwhole recombinant antibody molecule, are used for the expression of arecombinant antibody molecule. For example, mammalian cells such asChinese hamster ovary cells (CHO), in conjunction with a vector such asthe major intermediate early gene promoter element from humancytomegalovirus is an effective expression system for antibodies(Foecking et al., Gene 45:101 (1986); Cockett et al., Bio/Technology 8:2(1990)).

In bacterial systems, a number of expression vectors may beadvantageously selected depending upon the use intended for the antibodymolecule being expressed. For example, when a large quantity of such aprotein is to be produced, for the generation of pharmaceuticalcompositions of an antibody molecule, vectors which direct theexpression of high levels of fusion protein products that are readilypurified may be desirable. Such vectors include, but are not limited, tothe E. coli expression vector pUR278 (Ruther et al., EMBO J. 2:1791(1983)), in which the antibody coding sequence may be ligatedindividually into the vector in frame with the lac Z coding region sothat a fusion protein is produced; pIN vectors (Inouye & Inouye, NucleicAcids Res. 13:3101-3109 (1985); Van Heeke & Schuster, J. Biol. Chem.24:5503-5509 (1989)); and the like. pGEX vectors may also be used toexpress foreign polypeptides as fusion proteins with glutathioneS-transferase (GST). In general, such fusion proteins are soluble andcan easily be purified from lysed cells by adsorption and binding tomatrix glutathione-agarose beads followed by elution in the presence offree glutathione. The pGEX vectors are designed to include thrombin orfactor Xa protease cleavage sites so that the cloned target gene productcan be released from the GST moiety.

In an insect system, Autographa californica nuclear polyhedrosis virus(AcNPV) is used as a vector to express foreign genes. The virus grows inSpodoptera frugiperda cells. The antibody coding sequence may be clonedindividually into non-essential regions (for example the polyhedringene) of the virus and placed under control of an AcNPV promoter (forexample the polyhedrin promoter).

In mammalian host cells, a number of viral-based expression systems maybe utilized. In cases where an adenovirus is used as an expressionvector, the antibody coding sequence of interest may be ligated to anadenovirus transcription/translation control complex, e.g., the latepromoter and tripartite leader sequence. This chimeric gene may then beinserted in the adenovirus genome by in vitro or in vivo recombination.Insertion in a non-essential region of the viral genome (e.g., region E1or E3) will result in a recombinant virus that is viable and capable ofexpressing the antibody molecule in infected hosts. (E.g., see Logan &Shenk, Proc. Natl. Acad. Sci. USA 81:355-359 (1984)). Specificinitiation signals may also be required for efficient translation ofinserted antibody coding sequences. These signals include the ATGinitiation codon and adjacent sequences. Furthermore, the initiationcodon must be in phase with the reading frame of the desired codingsequence to ensure translation of the entire insert. These exogenoustranslational control signals and initiation codons can be of a varietyof origins, both natural and synthetic. The efficiency of expression maybe enhanced by the inclusion of appropriate transcription enhancerelements, transcription terminators, etc. (see Bittner et al., Methodsin Enzymol. 153:51-544 (1987)).

In addition, a host cell strain may be chosen which modulates theexpression of the inserted sequences, or modifies and processes the geneproduct in the specific fashion desired. Such modifications (e.g.,glycosylation) and processing (e.g., cleavage) of protein products maybe important for the function of the protein. Different host cells havecharacteristic and specific mechanisms for the post-translationalprocessing and modification of proteins and gene products. Appropriatecell lines or host systems can be chosen to ensure the correctmodification and processing of the foreign protein expressed. To thisend, eukaryotic host cells which possess the cellular machinery forproper processing of the primary transcript, glycosylation, andphosphorylation of the gene product may be used. Such mammalian hostcells include but are not limited to CHO, VERY, BHK, Hela, COS, MDCK,293, 3T3, W138, and in particular, breast cancer cell lines such as, forexample, BT483, Hs578T, HTB2, BT20 and T47D, and normal mammary glandcell lines such as, for example, CRL7030 and Hs578Bst.

For long-term, high-yield production of recombinant proteins, stableexpression is preferred. For example, cell lines which stably expressthe antibody molecule may be engineered. Rather than using expressionvectors which contain viral origins of replication, host cells can betransformed with DNA controlled by appropriate expression controlelements (e.g., promoter, enhancer, sequences, transcriptionterminators, polyadenylation sites, etc.), and a selectable marker.Following the introduction of the foreign DNA, engineered cells may beallowed to grow for 1-2 days in an enriched media, and then are switchedto a selective media. The selectable marker in the recombinant plasmidconfers resistance to the selection and allows cells to stably integratethe plasmid into their chromosomes and grow to form foci which in turncan be cloned and expanded into cell lines. This method mayadvantageously be used to engineer cell lines which express the antibodymolecule. Such engineered cell lines may be particularly useful inscreening and evaluation of compounds that interact directly orindirectly with the antibody molecule.

A number of selection systems may be used, including but not limited tothe herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223(1977)), hypoxanthine-guanine phosphoribosyltransferase (Szybalska &Szybalski, Proc. Natl. Acad. Sci. USA 48:202 (1992)), and adeninephosphoribosyltransferase (Lowy et al., Cell 22:817 (1980)) genes can beemployed in tk−, hgprt− or aprt− cells, respectively. Also,antimetabolite resistance can be used as the basis of selection for thefollowing genes: dhfr, which confers resistance to methotrexate (Wigleret al., Natl. Acad. Sci. USA 77:357 (1980); O'Hare et al., Proc. Natl.Acad. Sci. USA 78:1527 (1981)); gpt, which confers resistance tomycophenolic acid (Mulligan & Berg, Proc. Natl. Acad. Sci. USA 78:2072(1981)); neo, which confers resistance to the aminoglycoside G-418Clinical Pharmacy 12:488-505; Wu and Wu, Biotherapy 3:87-95 (1991);Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan,Science 260:926-932 (1993); and Morgan and Anderson, Ann. Rev. Biochem.62:191-217 (1993); May, 1993, TIB TECH 11(5):155-215); and hygro, whichconfers resistance to hygromycin (Santerre et al., Gene 30:147 (1984)).Methods commonly known in the art of recombinant DNA technology may beroutinely applied to select the desired recombinant clone, and suchmethods are described, for example, in Ausubel et al. (eds.), CurrentProtocols in Molecular Biology, John Wiley & Sons, NY (1993); Kriegler,Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY(1990); and in Chapters 12 and 13, Dracopoli et al. (eds), CurrentProtocols in Human Genetics, John Wiley & Sons, NY (1994);Colberre-Garapin et al., J. Mol. Biol. 150:1 (1981), which areincorporated by reference herein in their entireties.

The expression levels of an antibody molecule can be increased by vectoramplification (for a review, see Bebbington and Hentschel, The use ofvectors based on gene amplification for the expression of cloned genesin mammalian cells in DNA cloning, Vol. 3. (Academic Press, New York,1987)). When a marker in the vector system expressing antibody isamplifiable, increase in the level of inhibitor present in culture ofhost cell will increase the number of copies of the marker gene. Sincethe amplified region is associated with the antibody gene, production ofthe antibody will also increase (Crouse et al., Mol. Cell. Biol. 3:257(1983)).

The host cell may be co-transfected with two expression vectors of theinvention, the first vector encoding a heavy chain derived polypeptideand the second vector encoding a light chain derived polypeptide. Thetwo vectors may contain identical selectable markers which enable equalexpression of heavy and light chain polypeptides. Alternatively, asingle vector may be used which encodes, and is capable of expressing,both heavy and light chain polypeptides. In such situations, the lightchain should be placed before the heavy chain to avoid an excess oftoxic free heavy chain (Proudfoot, Nature 322:52 (1986); Kohler, Proc.Natl. Acad. Sci. USA 77:2197 (1980)). The coding sequences for the heavyand light chains may comprise cDNA or genomic DNA.

Once an antibody molecule of the invention has been produced by ananimal, chemically synthesized, or recombinantly expressed, it may bepurified by any method known in the art for purification of animmunoglobulin molecule, for example, by chromatography (e.g., ionexchange, affinity, particularly by affinity for the specific antigenafter Protein A, and sizing column chromatography), centrifugation,differential solubility, or by any other standard technique for thepurification of proteins. In addition, the antibodies of the presentinvention or fragments thereof can be fused to heterologous polypeptidesequences described herein or otherwise known in the art, to facilitatepurification.

The present invention encompasses antibodies recombinantly fused orchemically conjugated (including both covalent and non-covalentconjugations) to a polypeptide (or portion thereof, preferably at least10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids of thepolypeptide) of the present invention to generate fusion proteins. Thefusion does not necessarily need to be direct, but may occur throughlinker sequences. The antibodies may be specific for antigens other thanpolypeptides (or portion thereof, preferably at least 10, 20, 30, 40,50, 60, 70, 80, 90 or 100 amino acids of the polypeptide) of the presentinvention. For example, antibodies may be used to target thepolypeptides of the present invention to particular cell types, eitherin vitro or in vivo, by fusing or conjugating the polypeptides of thepresent invention to antibodies specific for particular cell surfacereceptors. Antibodies fused or conjugated to the polypeptides of thepresent invention may also be used in in vitro immunoassays andpurification methods using methods known in the art. See e.g., Harbor etal., supra, and PCT publication WO 93/21232; EP 439,095; Naramura etal., Immunol. Lett. 39:91-99 (1994); U.S. Pat. No. 5,474,981; Gillies etal., PNAS 89:1428-1432 (1992); Fell et al., J. Immunol. 146:2446-2452(1991), which are incorporated by reference in their entireties.

The present invention further includes compositions comprising thepolypeptides of the present invention fused or conjugated to antibodydomains other than the variable regions. For example, the polypeptidesof the present invention may be fused or conjugated to an antibody Fcregion, or portion thereof. The antibody portion fused to a polypeptideof the present invention may comprise the constant region, hinge region,CH1 domain, CH2 domain, and CH3 domain or any combination of wholedomains or portions thereof. The polypeptides may also be fused orconjugated to the above antibody portions to form multimers. Forexample, Fc portions fused to the polypeptides of the present inventioncan form dimers through disulfide bonding between the Fc portions.Higher multimeric forms can be made by fusing the polypeptides toportions of IgA and IgM. Methods for fusing or conjugating thepolypeptides of the present invention to antibody portions are known inthe art. See, e.g., U.S. Pat. Nos. 5,336,603; 5,622,929; 5,359,046;5,349,053; 5,447,851; 5,112,946; EP 307,434; EP 367,166; PCTpublications WO 96/04388; WO 91/06570; Ashkenazi et al., Proc. Natl.Acad. Sci. USA 88:10535-10539 (1991); Zheng et al., J. Immunol.154:5590-5600 (1995); and Vil et al., Proc. Natl. Acad. Sci. USA89:11337-11341 (1992) (said references incorporated by reference intheir entireties).

As discussed, supra, the polypeptides corresponding to a polypeptide,polypeptide fragment, or a variant of SEQ ID NO:2 may be fused orconjugated to the above antibody portions to increase the in vivo halflife of the polypeptides or for use in immunoassays using methods knownin the art. Further, the polypeptides corresponding to SEQ ID NO:2 maybe fused or conjugated to the above antibody portions to facilitatepurification. Also as discussed, supra, the polypeptides correspondingto a polypeptide, polypeptide fragment, or a variant of SEQ ID NO:19 maybe fused or conjugated to the above antibody portions to increase the invivo half life of the polypeptides or for use in immunoassays usingmethods known in the art. Moreover, the polypeptides corresponding toSEQ ID NO:19 may be fused or conjugated to the above antibody portionsto facilitate purification. One reported example describes chimericproteins consisting of the first two domains of the humanCD4-polypeptide and various domains of the constant regions of the heavyor light chains of mammalian immunoglobulins. (EP 394,827; Traunecker etal., Nature 331:84-86 (1988). The polypeptides of the present inventionfused or conjugated to an antibody having disulfide-linked dimericstructures (due to the IgG) may also be more efficient in binding andneutralizing other molecules, than the monomeric secreted protein orprotein fragment alone. (Fountoulakis et al., J. Biochem. 270:3958-3964(1995)). In many cases, the Fc part in a fusion protein is beneficial intherapy and diagnosis, and thus can result in, for example, improvedpharmacokinetic properties. (EP A 232,262). Alternatively, deleting theFc part after the fusion protein has been expressed, detected, andpurified, would be desired. For example, the Fc portion may hindertherapy and diagnosis if the fusion protein is used as an antigen forimmunizations. In drug discovery, for example, human proteins, such ashIL-5, have been fused with Fc portions for the purpose ofhigh-throughput screening assays to identify antagonists of hIL-5. (See,Bennett et al., J. Molecular Recognition 8:52-58 (1995); Johanson etal., J. Biol. Chem. 270:9459-9471 (1995).

Moreover, the antibodies or fragments thereof of the present inventioncan be fused to marker sequences, such as a peptide to facilitatepurification. In preferred embodiments, the marker amino acid sequenceis a hexa-histidine peptide, such as the tag provided in a pQE vector(QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311), amongothers, many of which are commercially available. As described in Gentzet al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), for instance,hexa-histidine provides for convenient purification of the fusionprotein. Other peptide tags useful for purification include, but are notlimited to, the “HA” tag, which corresponds to an epitope derived fromthe influenza hemagglutinin protein (Wilson et al., Cell 37:767 (1984))and the “flag” tag.

The present invention further encompasses antibodies or fragmentsthereof conjugated to a diagnostic or therapeutic agent. The antibodiescan be used diagnostically to, for example, monitor the development orprogression of a tumor as part of a clinical testing procedure to, e.g.,determine the efficacy of a given treatment regimen. Detection can befacilitated by coupling the antibody to a detectable substance. Examplesof detectable substances include various enzymes, prosthetic groups,fluorescent materials, luminescent materials, bioluminescent materials,radioactive materials, positron emitting metals using various positronemission tomographies, and nonradioactive paramagnetic metal ions. Thedetectable substance may be coupled or conjugated either directly to theantibody (or fragment thereof) or indirectly, through an intermediate(such as, for example, a linker known in the art) using techniques knownin the art. See, for example, U.S. Pat. No. 4,741,900 for metal ionswhich can be conjugated to antibodies for use as diagnostics accordingto the present invention. Examples of suitable enzymes includehorseradish peroxidase, alkaline phosphatase, beta-galactosidase, oracetylcholinesterase; examples of suitable prosthetic group complexesinclude streptavidin/biotin and avidin/biotin; examples of suitablefluorescent materials include umbelliferone, fluorescein, fluoresceinisothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansylchloride or phycoerythrin; an example of a luminescent material includesluminol; examples of bioluminescent materials include luciferase,luciferin, and aequorin; and examples of suitable radioactive materialinclude ¹²⁵I, ¹³¹I, ¹¹¹In or ⁹⁹Tc.

Further, an antibody or fragment thereof may be conjugated to atherapeutic moiety such as a cytotoxin, e.g., a cytostatic or cytocidalagent, a therapeutic agent or a radioactive metal ion, e.g.,alpha-emitters such as, for example, ²¹³Bi. A cytotoxin or cytotoxicagent includes any agent that is detrimental to cells. Examples includepaclitaxol, cytochalasin B, gramicidin D, ethidium bromide, emetine,mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin,doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone,mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids,procaine, tetracaine, lidocaine, propranolol, and puromycin and analogsor homologs thereof. Therapeutic agents include, but are not limited to,antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6-thioguanine,cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g.,mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) andlomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol,streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP)cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) anddoxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin),bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents(e.g., vincristine and vinblastine).

The conjugates of the invention can be used for modifying a givenbiological response, the therapeutic agent or drug moiety is not to beconstrued as limited to classical chemical therapeutic agents. Forexample, the drug moiety may be a protein or polypeptide possessing adesired biological activity. Such proteins may include, for example, atoxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin;a protein such as tumor necrosis factor, alpha-interferon,beta-interferon, nerve growth factor, platelet derived growth factor,tissue plasminogen activator, an apoptotic agent, e.g., TNF-alpha,TNF-beta, AIM I (See, International Publication No. WO 97/33899), AIM II(See, International Publication No. WO 97/34911), Fas Ligand (Takahashiet al., Int. Immunol., 6:1567-157 4 (1994)), VEGI (See, InternationalPublication No. WO 99/23105), CD40 Ligand, a thrombotic agent or ananti-angiogenic agent, e.g., angiostatin or endostatin; or, biologicalresponse modifiers such as, for example, lymphokines, interleukin-1(“IL-1”), interleukin-2 (“IL-2”), interleukin-6 (“IL-6”), granulocytemacrophage colony stimulating factor (“GM-CSF”), granulocyte colonystimulating factor (“G-CSF”), or other growth factors.

Antibodies may also be attached to solid supports, which areparticularly useful for immunoassays or purification of the targetantigen. Such solid supports include, but are not limited to, glass,cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride orpolypropylene.

Techniques for conjugating such therapeutic moiety to antibodies arewell known, see, e.g., Amon et al., “Monoclonal Antibodies ForImmunotargeting Of Drugs In Cancer Therapy”, in Monoclonal AntibodiesAnd Cancer Therapy, Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss,Inc. 1985); Hellstrom et al., “Antibodies For Drug Delivery”, inControlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp. 623-53(Marcel Dekker, Inc. 1987); Thorpe, “Antibody Carriers Of CytotoxicAgents In Cancer Therapy: A Review”, in Monoclonal Antibodies '84:Biological And Clinical Applications, Pinchera et al. (eds.), pp.475-506 (1985); “Analysis, Results, And Future Prospective Of TheTherapeutic Use Of Radiolabeled Antibody in Cancer Therapy”, inMonoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al.(eds.), pp. 303-16 (Academic Press 1985), and Thorpe et al., “ThePreparation And Cytotoxic Properties Of Antibody-Toxin Conjugates”,Immunol. Rev. 62:119-58 (1982).

Alternatively, an antibody can be conjugated to a second antibody toform an antibody heteroconjugate as described by Segal in U.S. Pat. No.4,676,980, which is incorporated herein by reference in its entirety.

An antibody, with or without a therapeutic moiety conjugated to it,administered alone or in combination with cytotoxic factor(s) and/orcytokine(s) can be used as a therapeutic.

Immunophenotyping

The antibodies of the invention may be utilized for immunophenotyping ofcell lines and biological samples. The translation product of the geneof the present invention may be useful as a cell specific marker, ormore specifically as a cellular marker that is differentially expressedat various stages of differentiation and/or maturation of particularcell types. Monoclonal antibodies directed against a specific epitope,or combination of epitopes, will allow for the screening of cellularpopulations expressing the marker. Various techniques can be utilizedusing monoclonal antibodies to screen for cellular populationsexpressing the marker(s), and include magnetic separation usingantibody-coated magnetic beads, “panning” with antibody attached to asolid matrix (i.e., plate), and flow cytometry (See, e.g., U.S. Pat. No.5,985,660; and Morrison et al., Cell, 96:737-49 (1999)).

These techniques allow for the screening of particular populations ofcells, such as might be found with hematological malignancies (i.e.minimal residual disease (MRD) in acute leukemic patients) and“non-self” cells in transplantations to prevent Graft-versus-HostDisease (GVHD). Alternatively, these techniques allow for the screeningof hematopoietic stem and progenitor cells capable of undergoingproliferation and/or differentiation, as might be found in humanumbilical cord blood.

Assays for Antibody Binding

The antibodies of the invention may be assayed for immunospecificbinding by any method known in the art. The immunoassays which can beused, include but are not limited to, competitive and non-competitiveassay systems using techniques such as western blots, radioimmunoassays,ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays,immunoprecipitation assays, precipitin reactions, gel diffusionprecipitin reactions, immunodiffusion assays, agglutination assays,complement-fixation assays, immunoradiometric assays, fluorescentimmunoassays, protein A immunoassays, to name but a few. Such assays areroutine and well known in the art (see, e.g., Ausubel et al, eds, 1994,Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc.,New York, which is incorporated by reference herein in its entirety).Exemplary immunoassays are described briefly below (but are not intendedby way of limitation).

Immunoprecipitation protocols generally comprise lysing a population ofcells in a lysis buffer such as RIPA buffer (1% NP-40 or Triton X-100,1% sodium deoxycholate, 0.1% SDS, 0.15 M NaCl, 0.01 M sodium phosphateat pH 7.2, 1% Trasylol) supplemented with protein phosphatase and/orprotease inhibitors (e.g., EDTA, PMSF, aprotinin, sodium vanadate),adding the antibody of interest to the cell lysate, incubating for aperiod of time (e.g., 1-4 hours) at 4° C., adding protein A and/orprotein G sepharose beads to the cell lysate, incubating for about anhour or more at 4° C., washing the beads in lysis buffer andresuspending the beads in SDS/sample buffer. The ability of the antibodyof interest to immunoprecipitate a particular antigen can be assessedby, e.g., western blot analysis. One of skill in the art would beknowledgeable as to the parameters that can be modified to increase thebinding of the antibody to an antigen and decrease the background (e.g.,pre-clearing the cell lysate with sepharose beads). For furtherdiscussion regarding immunoprecipitation protocols see, e.g., Ausubel etal, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, JohnWiley & Sons, Inc., New York at 10.16.1.

Western blot analysis generally comprises preparing protein samples,electrophoresis of the protein samples in a polyacrylamide gel (e.g.,8%-20% SDS-PAGE depending on the molecular weight of the antigen),transferring the protein sample from the polyacrylamide gel to amembrane such as nitrocellulose, PVDF or nylon, blocking the membrane inblocking solution (e.g., PBS with 3% BSA or non-fat milk), washing themembrane in washing buffer (e.g., PBS-Tween 20), blocking the membranewith primary antibody (the antibody of interest) diluted in blockingbuffer, washing the membrane in washing buffer, blocking the membranewith a secondary antibody (which recognizes the primary antibody, e.g.,an anti-human antibody) conjugated to an enzymatic substrate (e.g.,horseradish peroxidase or alkaline phosphatase) or radioactive molecule(e.g., ³²P or ¹²⁵I) diluted in blocking buffer, washing the membrane inwash buffer, and detecting the presence of the antigen. One of skill inthe art would be knowledgeable as to the parameters that can be modifiedto increase the signal detected and to reduce the background noise. Forfurther discussion regarding western blot protocols see, e.g., Ausubelet al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, JohnWiley & Sons, Inc., New York at 10.8.1.

ELISAs comprise preparing antigen, coating the well of a 96 wellmicrotiter plate with the antigen, adding the antibody of interestconjugated to a detectable compound such as an enzymatic substrate(e.g., horseradish peroxidase or alkaline phosphatase) to the well andincubating for a period of time, and detecting the presence of theantigen. In ELISAs the antibody of interest does not have to beconjugated to a detectable compound; instead, a second antibody (whichrecognizes the antibody of interest) conjugated to a detectable compoundmay be added to the well. Further, instead of coating the well with theantigen, the antibody may be coated to the well. In this case, a secondantibody conjugated to a detectable compound may be added following theaddition of the antigen of interest to the coated well. One of skill inthe art would be knowledgeable as to the parameters that can be modifiedto increase the signal detected as well as other variations of ELISAsknown in the art. For further discussion regarding ELISAs see, e.g.,Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol.1, John Wiley & Sons, Inc., New York at 11.2.1.

The binding affinity of an antibody to an antigen and the off-rate of anantibody-antigen interaction can be determined by competitive bindingassays. One example of a competitive binding assay is a radioimmunoassaycomprising the incubation of labeled antigen (e.g., ³H or ¹²⁵I) with theantibody of interest in the presence of increasing amounts of unlabeledantigen, and the detection of the antibody bound to the labeled antigen.The affinity of the antibody of interest for a particular antigen andthe binding off-rates can be determined from the data by scatchard plotanalysis. Competition with a second antibody can also be determinedusing radioimmunoassays. In this case, the antigen is incubated withantibody of interest conjugated to a labeled compound (e.g., ³H or ¹²⁵I)in the presence of increasing amounts of an unlabeled second antibody.

Therapeutic Uses

The present invention is further directed to antibody-based therapieswhich involve administering antibodies of the invention to an animal,preferably a mammal, and most preferably a human, patient for treatingone or more of the disclosed diseases, disorders, or conditions.Therapeutic compounds of the invention include, but are not limited to,antibodies of the invention (including fragments, analogs andderivatives thereof as described herein) and nucleic acids encodingantibodies of the invention (including fragments, analogs andderivatives thereof and anti-idiotypic antibodies as described herein).The antibodies of the invention can be used to treat, inhibit or preventdiseases, disorders or conditions associated with aberrant expressionand/or activity of a polypeptide of the invention, including, but notlimited to, any one or more of the diseases, disorders, or conditionsdescribed herein (e.g., autoimmune diseases, disorders, or conditionsassociated with such diseases or disorders, including, but not limitedto, autoimmune hemolytic anemia, autoimmune neonatal thrombocytopenia,idiopathic thrombocytopenia purpura, autoimmunocytopenia, hemolyticanemia, antiphospholipid syndrome, dermatitis, allergicencephalomyelitis, myocarditis, relapsing polychondritis, rheumaticheart disease, glomerulonephritis (e.g., IgA nephropathy), MultipleSclerosis, Neuritis, Uveitis Ophthalmia, Polyendocrinopathies, Purpura(e.g., Henloch-Scoenlein purpura), Reiter's Disease, Stiff-Man Syndrome,Autoimmune Pulmonary Inflammation, Guillain-Barre Syndrome, insulindependent diabetes mellitus, and autoimmune inflammatory eye, autoimmunethyroiditis, hypothyroidism (i.e., Hashimoto's thyroiditis, systemiclupus erythematosus, Goodpasture's syndrome, Pemphigus, Receptorautoimmunities such as, for example, (a) Graves' Disease, (b) MyastheniaGravis, and (c) insulin resistance, autoimmune hemolytic anemia,autoimmune thrombocytopenic purpura, rheumatoid arthritis, schlerodermawith anti-collagen antibodies, mixed connective tissue disease,polymyositis/dermatomyositis, pernicious anemia, idiopathic Addison'sdisease, infertility, glomerulonephritis such as primaryglomerulonephritis and IgA nephropathy, bullous pemphigoid, Sjogren'ssyndrome, diabetes mellitus, and adrenergic drug resistance (includingadrenergic drug resistance with asthma or cystic fibrosis), chronicactive hepatitis, primary biliary cirrhosis, other endocrine glandfailure, vitiligo, vasculitis, post-MI, cardiotomy syndrome, urticaria,atopic dermatitis, asthma, inflammatory myopathies, and otherinflammatory, granulomatous, degenerative, and atrophic disorders).

In a specific embodiment, antibodies of the invention are be used totreat, inhibit, prognose, diagnose or prevent rheumatoid arthritis.

In another specific embodiment, antibodies of the invention are used totreat, inhibit, prognose, diagnose or prevent systemic lupuserythematosis.

The treatment and/or prevention of diseases, disorders, or conditionsassociated with aberrant expression and/or activity of a polypeptide ofthe invention includes, but is not limited to, alleviating symptomsassociated with those diseases, disorders or conditions. The antibodiesof the invention may also be used to target and kill cells expressingNeutrokine-alpha on their surface and/or cells having Neutrokine-alphabound to their surface. Antibodies of the invention may be provided inpharmaceutically acceptable compositions as known in the art or asdescribed herein.

A summary of the ways in which the antibodies of the present inventionmay be used therapeutically includes binding polynucleotides orpolypeptides of the present invention locally or systemically in thebody or by direct cytotoxicity of the antibody, e.g., as mediated bycomplement (CDC) or by effector cells (ADCC). Some of these approachesare described in more detail below. Armed with the teachings providedherein, one of ordinary skill in the art will know how to use theantibodies of the present invention for diagnostic, monitoring ortherapeutic purposes without undue experimentation.

The antibodies of this invention may be advantageously utilized incombination with other monoclonal or chimeric antibodies, or withlymphokines or hematopoietic growth factors (such as, e.g., IL-2, IL-3and IL-7), for example, which serve to increase the number or activityof effector cells which interact with the antibodies.

The antibodies of the invention may be administered alone or incombination with other types of treatments (e.g., radiation therapy,chemotherapy, hormonal therapy, immunotherapy, anti-tumor agents,antibiotics, and immunoglobulin). Generally, administration of productsof a species origin or species reactivity (in the case of antibodies)that is the same species as that of the patient is preferred. Thus, in apreferred embodiment, human antibodies, fragments derivatives, analogs,or nucleic acids, are administered to a human patient for therapy orprophylaxis.

It is preferred to use high affinity and/or potent in vivo inhibitingand/or neutralizing antibodies against polypeptides or polynucleotidesof the present invention, fragments or regions thereof, for bothimmunoassays directed to and therapy of disorders related topolynucleotides or polypeptides, including fragments thereof, of thepresent invention. Such antibodies, fragments, or regions, willpreferably have an affinity for polynucleotides or polypeptides of theinvention, including fragments thereof. Preferred binding affinitiesinclude those with a dissociation constant or Kd less than 5×10⁻⁵ M,10⁻⁵ M, 5×10⁻⁶ M, 10⁻⁶ M, 5×10⁻⁷ M, 10⁻⁷ M, 5×10⁻⁸ M, 10⁻⁸ M, 5×10⁻⁹ M,10⁻⁹ M, 5×10⁻¹⁰ M, 10⁻¹⁰ M, 5×10⁻¹¹ M, 10⁻¹¹ M, 5×10⁻¹² M, 10⁻¹² M,5×10⁻¹³ M, 10⁻¹³ M, 5×10⁻¹⁴ M, 10⁻¹⁴ M, 5×10⁻¹⁵ M, and 10⁻¹⁵ M.

Gene Therapy

In a specific embodiment, nucleic acids comprising sequences encodingantibodies or functional derivatives thereof, are administered to treat,inhibit or prevent a disease or disorder associated with aberrantexpression and/or activity of a polypeptide of the invention, by way ofgene therapy. Gene therapy refers to therapy performed by theadministration to a subject of an expressed or expressible nucleic acid.In this embodiment of the invention, the nucleic acids produce theirencoded protein that mediates a therapeutic effect.

Any of the methods for gene therapy available in the art can be usedaccording to the present invention. Exemplary methods are describedbelow.

For general reviews of the methods of gene therapy, see Goldspiel etal., Clinical Pharmacy 12:488-505 (1993); Wu and Wu, Biotherapy 3:87-95(1991); Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993);Mulligan, Science 260:926-932 (1993); and Morgan and Anderson, Ann. Rev.Biochem. 62:191-217 (1993); May, TIBTECH 11(5):155-215 (1993). Methodscommonly known in the art of recombinant DNA technology which can beused are described in Ausubel et al. (eds.), Current Protocols inMolecular Biology, John Wiley & Sons, NY (1993); and Kriegler, GeneTransfer and Expression, A Laboratory Manual, Stockton Press, NY (1990).

In a preferred embodiment, the compound comprises nucleic acid sequencesencoding an antibody, said nucleic acid sequences being part ofexpression vectors that express the antibody or fragments or chimericproteins or heavy or light chains thereof in a suitable host. Inparticular, such nucleic acid sequences have promoters operably linkedto the antibody coding region, said promoter being inducible orconstitutive, and, optionally, tissue-specific. In another particularembodiment, nucleic acid molecules are used in which the antibody codingsequences and any other desired sequences are flanked by regions thatpromote homologous recombination at a desired site in the genome, thusproviding for intrachromosomal expression of the antibody encodingnucleic acids (Koller and Smithies, Proc. Natl. Acad. Sci. USA86:8932-8935 (1989); Zijlstra et al., Nature 342:435-438 (1989). Inspecific embodiments, the expressed antibody molecule is a single chainantibody; alternatively, the nucleic acid sequences include sequencesencoding both the heavy and light chains, or fragments thereof, of theantibody.

Delivery of the nucleic acids into a patient may be either direct, inwhich case the patient is directly exposed to the nucleic acid ornucleic acid-carrying vectors, or indirect, in which case, cells arefirst transformed with the nucleic acids in vitro, then transplantedinto the patient. These two approaches are known, respectively, as invivo or ex vivo gene therapy.

In a specific embodiment, the nucleic acid sequences are directlyadministered in vivo, where it is expressed to produce the encodedproduct. This can be accomplished by any of numerous methods known inthe art, e.g., by constructing them as part of an appropriate nucleicacid expression vector and administering it so that they becomeintracellular, e.g., by infection using defective or attenuatedretrovirals or other viral vectors (see U.S. Pat. No. 4,980,286), or bydirect injection of naked DNA, or by use of microparticle bombardment(e.g., a gene gun; Biolistic, Dupont), or coating with lipids orcell-surface receptors or transfecting agents, encapsulation inliposomes, microparticles, or microcapsules, or by administering them inlinkage to a peptide which is known to enter the nucleus, byadministering it in linkage to a ligand subject to receptor-mediatedendocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432 (1987))(which can be used to target cell types specifically expressing thereceptors), etc. In another embodiment, nucleic acid-ligand complexescan be formed in which the ligand comprises a fusogenic viral peptide todisrupt endosomes, allowing the nucleic acid to avoid lysosomaldegradation. In yet another embodiment, the nucleic acid can be targetedin vivo for cell specific uptake and expression, by targeting a specificreceptor (see, e.g., PCT Publications WO 92/06180; WO 92/22635;WO92/20316; WO93/14188, WO 93/20221). Alternatively, the nucleic acidcan be introduced intracellularly and incorporated within host cell DNAfor expression, by homologous recombination (Koller and Smithies, Proc.Natl. Acad. Sci. USA 86:8932-8935 (1989); Zijlstra et al., Nature342:435-438 (1989)).

In a specific embodiment, viral vectors that contain nucleic acidsequences encoding an antibody of the invention are used. For example, aretroviral vector can be used (see Miller et al., Meth. Enzymol.217:581-599 (1993)). These retroviral vectors contain the componentsnecessary for the correct packaging of the viral genome and integrationinto the host cell DNA. The nucleic acid sequences encoding the antibodyto be used in gene therapy are cloned into one or more vectors, whichfacilitates delivery of the gene into a patient. More detail aboutretroviral vectors can be found in Boesen et al., Biotherapy 6:291-302(1994), which describes the use of a retroviral vector to deliver themdr1 gene to hematopoietic stem cells in order to make the stem cellsmore resistant to chemotherapy. Other references illustrating the use ofretroviral vectors in gene therapy are: Clowes et al., J. Clin. Invest.93:644-651 (1994); Kiem et al., Blood 83:1467-1473 (1994); Salmons andGunzberg, Human Gene Therapy 4:129-141 (1993); and Grossman and Wilson,Curr. Opin. in Genetics and Devel. 3:110-114 (1993).

Adenoviruses are other viral vectors that can be used in gene therapy.Adenoviruses are especially attractive vehicles for delivering genes torespiratory epithelia. Adenoviruses naturally infect respiratoryepithelia where they cause a mild disease. Other targets foradenovirus-based delivery systems are liver, the central nervous system,endothelial cells, and muscle. Adenoviruses have the advantage of beingcapable of infecting non-dividing cells. Kozarsky and Wilson, CurrentOpinion in Genetics and Development 3:499-503 (1993) present a review ofadenovirus-based gene therapy. Bout et al., Human Gene Therapy 5:3-10(1994) demonstrated the use of adenovirus vectors to transfer genes tothe respiratory epithelia of rhesus monkeys. Other instances of the useof adenoviruses in gene therapy can be found in Rosenfeld et al.,Science 252:431-434 (1991); Rosenfeld et al., Cell 68:143-155 (1992);Mastrangeli et al., J. Clin. Invest. 91:225-234 (1993); PCT PublicationWO94/12649; and Wang, et al., Gene Therapy 2:775-783 (1995). In apreferred embodiment, adenovirus vectors are used.

Adeno-associated virus (AAV) has also been proposed for use in genetherapy (Walsh et al., Proc. Soc. Exp. Biol. Med. 204:289-300 (1993);U.S. Pat. No. 5,436,146).

Another approach to gene therapy involves transferring a gene to cellsin tissue culture by such methods as electroporation, lipofection,calcium phosphate mediated transfection, or viral infection. Usually,the method of transfer includes the transfer of a selectable marker tothe cells. The cells are then placed under selection to isolate thosecells that have taken up and are expressing the transferred gene. Thosecells are then delivered to a patient.

In this embodiment, the nucleic acid is introduced into a cell prior toadministration in vivo of the resulting recombinant cell. Suchintroduction can be carried out by any method known in the art,including but not limited to transfection, electroporation,microinjection, infection with a viral or bacteriophage vectorcontaining the nucleic acid sequences, cell fusion, chromosome-mediatedgene transfer, microcell-mediated gene transfer, spheroplast fusion,etc. Numerous techniques are known in the art for the introduction offoreign genes into cells (see, e.g., Loeffler and Behr, Meth. Enzymol.217:599-618 (1993); Cohen et al., Meth. Enzymol. 217:618-644 (1993);Clin., Pharmac. Ther. 29:69-92m (1985) and may be used in accordancewith the present invention, provided that the necessary developmentaland physiological functions of the recipient cells are not disrupted.The technique should provide for the stable transfer of the nucleic acidto the cell, so that the nucleic acid is expressible by the cell andpreferably heritable and expressible by its cell progeny.

The resulting recombinant cells can be delivered to a patient by variousmethods known in the art. Recombinant blood cells (e.g., hematopoieticstem or progenitor cells) are preferably administered intravenously. Theamount of cells envisioned for use depends on the desired effect,patient state, etc., and can be determined by one skilled in the art.

Cells into which a nucleic acid can be introduced for purposes of genetherapy encompass any desired, available cell type, and include, but arenot limited to, epithelial cells, endothelial cells, keratinocytes,fibroblasts, muscle cells, hepatocytes; blood cells such as Tlymphocytes, B lymphocytes, monocytes, macrophages, neutrophils,eosinophils, megakaryocytes, granulocytes; various stem or progenitorcells, in particular hematopoietic stem or progenitor cells, e.g., asobtained from bone marrow, umbilical cord blood, peripheral blood, fetalliver, etc.

In a preferred embodiment, the cell used for gene therapy is autologousto the patient.

In an embodiment in which recombinant cells are used in gene therapy,nucleic acid sequences encoding an antibody are introduced into thecells such that they are expressible by the cells or their progeny, andthe recombinant cells are then administered in vivo for therapeuticeffect. In a specific embodiment, stem or progenitor cells are used. Anystem and/or progenitor cells which can be isolated and maintained invitro can potentially be used in accordance with this embodiment of thepresent invention (see e.g., PCT Publication WO 94/08598; Stemple andAnderson, Cell 71:973-985 (1992); Rheinwald, Meth. Cell Bio. 21A:229(1980); and Pittelkow and Scott, Mayo Clinic Proc. 61:771 (1986)).

In a specific embodiment, the nucleic acid to be introduced for purposesof gene therapy comprises an inducible promoter operably linked to thecoding region, such that expression of the nucleic acid is controllableby controlling the presence or absence of the appropriate inducer oftranscription.

Demonstration of Therapeutic or Prophylactic Activity

The compounds or pharmaceutical compositions of the invention arepreferably tested in vitro, and then in vivo for the desired therapeuticor prophylactic activity, prior to use in humans. For example, in vitroassays to demonstrate the therapeutic or prophylactic utility of acompound or pharmaceutical composition include, the effect of a compoundon a cell line or a patient tissue sample. The effect of the compound orcomposition on the cell line and/or tissue sample can be determinedutilizing techniques known to those of skill in the art including, butnot limited to, rosette formation assays and cell lysis assays. Inaccordance with the invention, in vitro assays which can be used todetermine whether administration of a specific compound is indicated,include in vitro cell culture assays in which a patient tissue sample isgrown in culture, and exposed to or otherwise administered a compound,and the effect of such compound upon the tissue sample is observed.

Therapeutic and/or Prophylactic Administration and Composition

The invention provides methods of treatment, inhibition and prophylaxisby administration to a subject of an effective amount of a compound orpharmaceutical composition of the invention, preferably an antibody ofthe invention. In a preferred embodiment, the compound is substantiallypurified (e.g., substantially free from substances that limit its effector produce undesired side effects). The subject is preferably an animal,including but not limited to animals such as cows, pigs, horses,chickens, cats, dogs, etc., and is preferably a mammal, and mostpreferably human.

Formulations and methods of administration that can be employed when thecompound comprises a nucleic acid or an immunoglobulin are describedabove; additional appropriate formulations and routes of administrationcan be selected from among those described herein below.

Various delivery systems are known and can be used to administer acompound of the invention, e.g., encapsulation in liposomes,microparticles, microcapsules, recombinant cells capable of expressingthe compound, receptor-mediated endocytosis (see, e.g., Wu and Wu, J.Biol. Chem. 262:4429-4432 (1987)), construction of a nucleic acid aspart of a retroviral or other vector, etc. Methods of introductioninclude but are not limited to intradermal, intramuscular,intraperitoneal, intravenous, subcutaneous, intranasal, epidural, andoral routes. The compounds or compositions may be administered by anyconvenient route, for example by infusion or bolus injection, byabsorption through epithelial or mucocutaneous linings (e.g., oralmucosa, rectal and intestinal mucosa, etc.) and may be administeredtogether with other biologically active agents. Administration can besystemic or local. In addition, it may be desirable to introduce thepharmaceutical compounds or compositions of the invention into thecentral nervous system by any suitable route, including intraventricularand intrathecal injection; intraventricular injection may be facilitatedby an intraventricular catheter, for example, attached to a reservoir,such as an Ommaya reservoir. Pulmonary administration can also beemployed, e.g., by use of an inhaler or nebulizer, and formulation withan aerosolizing agent.

In a specific embodiment, it may be desirable to administer thepharmaceutical compounds or compositions of the invention locally to thearea in need of treatment; this may be achieved by, for example, and notby way of limitation, local infusion during surgery, topicalapplication, e.g., in conjunction with a wound dressing after surgery,by injection, by means of a catheter, by means of a suppository, or bymeans of an implant, said implant being of a porous, non-porous, orgelatinous material, including membranes, such as sialastic membranes,or fibers. Preferably, when administering a protein, including anantibody, of the invention, care must be taken to use materials to whichthe protein does not absorb.

In another embodiment, the compound or composition can be delivered in avesicle, in particular a liposome (see Langer, Science 249:1527-1533(1990); Treat et al., in Liposomes in the Therapy of Infectious Diseaseand Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp.353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generallyibid.)

In yet another embodiment, the compound or composition can be deliveredin a controlled release system. In one embodiment, a pump may be used(see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987);Buchwald et al., Surgery 88:507 (1980); Saudek et al., N. Engl. J. Med.321:574 (1989)). In another embodiment, polymeric materials can be used(see Medical Applications of Controlled Release, Langer and Wise (eds.),CRC Press, Boca Raton, Fla. (1974); Controlled Drug Bioavailability,Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, NewYork (1984); Ranger and Peppas, J., Macromol. Sci. Rev. Macromol. Chem.23:61 (1983); see also Levy et al., Science 228:190 (1985); During etal., Ann. Neurol. 25:351 (1989); Howard et al., J. Neurosurg. 71:105(1989)). In yet another embodiment, a controlled release system can beplaced in proximity of the therapeutic target, i.e., the brain, thusrequiring only a fraction of the systemic dose (see, e.g., Goodson, inMedical Applications of Controlled Release, supra, vol. 2, pp. 115-138(1984)).

Other controlled release systems are discussed in the review by Langer(Science 249:1527-1533 (1990)).

In a specific embodiment where the compound of the invention is anucleic acid encoding a protein, the nucleic acid can be administered invivo to promote expression of its encoded protein, by constructing it aspart of an appropriate nucleic acid expression vector and administeringit so that it becomes intracellular, e.g., by use of a retroviral vector(see U.S. Pat. No. 4,980,286), or by direct injection, or by use ofmicroparticle bombardment (e.g., a gene gun; Biolistic, Dupont), orcoating with lipids or cell-surface receptors or transfecting agents, orby administering it in linkage to a homeobox-like peptide which is knownto enter the nucleus (see e.g., Joliot et al., Proc. Natl. Acad. Sci.USA 88:1864-1868 (1991)), etc. Alternatively, a nucleic acid can beintroduced intracellularly and incorporated within host cell DNA forexpression, by homologous recombination.

The present invention also provides pharmaceutical compositions. Suchcompositions comprise a therapeutically effective amount of a compound,and a pharmaceutically acceptable carrier. In a specific embodiment, theterm “pharmaceutically acceptable” means approved by a regulatory agencyof the Federal or a state government or listed in the U.S. Pharmacopeiaor other generally recognized pharmacopeia for use in animals, and moreparticularly in humans. The term “carrier” refers to a diluent,adjuvant, excipient, or vehicle with which the therapeutic isadministered. Such pharmaceutical carriers can be sterile liquids, suchas water and oils, including those of petroleum, animal, vegetable orsynthetic origin, such as peanut oil, soybean oil, mineral oil, sesameoil and the like. Water is a preferred carrier when the pharmaceuticalcomposition is administered intravenously. Saline solutions and aqueousdextrose and glycerol solutions can also be employed as liquid carriers,particularly for injectable solutions. Suitable pharmaceuticalexcipients include starch, glucose, lactose, sucrose, gelatin, malt,rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate,talc, sodium chloride, dried skim milk, glycerol, propylene, glycol,water, ethanol and the like. The composition, if desired, can alsocontain minor amounts of wetting or emulsifying agents, or pH bufferingagents. These compositions can take the form of solutions, suspensions,emulsion, tablets, pills, capsules, powders, sustained-releaseformulations and the like. The composition can be formulated as asuppository, with traditional binders and carriers such astriglycerides. Oral formulation can include standard carriers such aspharmaceutical grades of mannitol, lactose, starch, magnesium stearate,sodium saccharine, cellulose, magnesium carbonate, etc. Examples ofsuitable pharmaceutical carriers are described in “Remington'sPharmaceutical Sciences” by E. W. Martin. Such compositions will containa therapeutically effective amount of the compound, preferably inpurified form, together with a suitable amount of carrier so as toprovide the form for proper administration to the patient. Theformulation should suit the mode of administration.

In a preferred embodiment, the composition is formulated in accordancewith routine procedures as a pharmaceutical composition adapted forintravenous administration to human beings. Typically, compositions forintravenous administration are solutions in sterile isotonic aqueousbuffer. Where necessary, the composition may also include a solubilizingagent and a local anesthetic such as lignocaine to ease pain at the siteof the injection. Generally, the ingredients are supplied eitherseparately or mixed together in unit dosage form, for example, as a drylyophilized powder or water free concentrate in a hermetically sealedcontainer such as an ampoule or sachette indicating the quantity ofactive agent. Where the composition is to be administered by infusion,it can be dispensed with an infusion bottle containing sterilepharmaceutical grade water or saline. Where the composition isadministered by injection, an ampoule of sterile water for injection orsaline can be provided so that the ingredients may be mixed prior toadministration.

The compounds of the invention can be formulated as neutral or saltforms. Pharmaceutically acceptable salts include those formed withanions such as those derived from hydrochloric, phosphoric, acetic,oxalic, tartaric acids, etc., and those formed with cations such asthose derived from sodium, potassium, ammonium, calcium, ferrichydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol,histidine, procaine, etc.

The amount of the compound of the invention which will be effective inthe treatment, inhibition and prevention of a disease or disorderassociated with aberrant expression and/or activity of a polypeptide ofthe invention can be determined by standard clinical techniques. Inaddition, in vitro assays may optionally be employed to help identifyoptimal dosage ranges. The precise dose to be employed in theformulation will also depend on the route of administration, and theseriousness of the disease or disorder, and should be decided accordingto the judgment of the practitioner and each patient's circumstances.Effective doses may be extrapolated from dose-response curves derivedfrom in vitro or animal model test systems.

For antibodies, the dosage administered to a patient is typically 0.1mg/kg to 100 mg/kg of the patient's body weight. Preferably, the dosageadministered to a patient is between 0.1 mg/kg and 20 mg/kg of thepatient's body weight, more preferably 1 mg/kg to 10 mg/kg of thepatient's body weight. Generally, human antibodies have a longerhalf-life within the human body than antibodies from other species dueto the immune response to the foreign polypeptides. Thus, lower dosagesof human antibodies and less frequent administration is often possible.Further, the dosage and frequency of administration of antibodies of theinvention may be reduced by enhancing uptake and tissue penetration(e.g., into the brain) of the antibodies by modifications such as, forexample, lipidation.

The invention also provides a pharmaceutical pack or kit comprising oneor more containers filled with one or more of the ingredients of thepharmaceutical compositions of the invention. Optionally associated withsuch container(s) can be a notice in the form prescribed by agovernmental agency regulating the manufacture, use or sale ofpharmaceuticals or biological products, which notice reflects approvalby the agency of manufacture, use or sale for human administration.

Diagnosis and Imaging

Labeled antibodies, and derivatives and analogs thereof, whichspecifically bind to a polypeptide of interest can be used fordiagnostic purposes to detect, diagnose, or monitor diseases and/ordisorders associated with the aberrant expression and/or activity of apolypeptide of the invention. The invention provides for the detectionof aberrant expression of a polypeptide of interest, comprising (a)assaying the expression of the polypeptide of interest in cells or bodyfluid of an individual using one or more antibodies specific to thepolypeptide interest and (b) comparing the level of gene expression witha standard gene expression level, whereby an increase or decrease in theassayed polypeptide gene expression level compared to the standardexpression level is indicative of aberrant expression.

The invention provides a diagnostic assay for diagnosing a disorder,comprising (a) assaying the expression of the polypeptide of interest incells or body fluid of an individual using one or more antibodiesspecific to the polypeptide interest and (b) comparing the level of geneexpression with a standard gene expression level, whereby an increase ordecrease in the assayed polypeptide gene expression level compared tothe standard expression level is indicative of a particular disorder.With respect to cancer, the presence of a relatively high amount oftranscript in biopsied tissue from an individual may indicate apredisposition for the development of the disease, or may provide ameans for detecting the disease prior to the appearance of actualclinical symptoms. A more definitive diagnosis of this type may allowhealth professionals to employ preventative measures or aggressivetreatment earlier thereby preventing the development or furtherprogression of the cancer.

Antibodies of the invention can be used to assay protein levels in abiological sample using classical immunohistological methods known tothose of skill in the art (e.g., see Jalkanen, et al., J. Cell. Biol.101:976-985 (1985); Jalkanen, et al., J. Cell. Biol. 105:3087-3096(1987)). Other antibody-based methods useful for detecting protein geneexpression include immunoassays, such as the enzyme linked immunosorbentassay (ELISA) and the radioimmunoassay (RIA). Suitable antibody assaylabels are known in the art and include enzyme labels, such as, glucoseoxidase; radioisotopes, such as iodine (¹³¹I, ¹²⁵I, ¹²³I, ¹²¹I), carbon(¹⁴C), sulfur (³⁵S), tritium (³H), indium (^(115m)In, ^(113m)In, ¹¹²In,¹¹¹In), and technetium (⁹⁹Tc, ^(99m)Tc), thallium Ti), gallium (⁶⁸Ga,⁶⁷Ga), palladium (¹⁰³Pd), molybdenum (⁹⁹Mo), xenon (¹³³Xe), fluorine(¹⁸F) ¹⁵³Sm, ¹⁷⁷Lu, ¹⁵⁹Gd, ¹⁴⁹Pm, ¹⁴⁰La, ¹⁷⁵Yb, ¹⁶⁶Ho, ⁹⁰Y, ⁴⁷Sc, ¹⁸⁶Re,¹⁸⁸Re, ¹⁴²Pr, ¹⁰⁵Rh, ⁹⁷Ru; luminescent labels, such as luminol; andfluorescent labels, such as fluorescein and rhodamine, and biotin.

Techniques known in the art may be applied to label antibodies of theinvention. Such techniques include, but are not limited to, the use ofbifunctional conjugating agents (see e.g., U.S. Pat. Nos. 5,756,065;5,714,631; 5,696,239; 5,652,361; 5,505,931; 5,489,425; 5,435,990;5,428,139; 5,342,604; 5,274,119; 4,994,560; and 5,808,003; the contentsof each of which are hereby incorporated by reference in its entirety).

One embodiment of the invention is the detection and diagnosis of adisease or disorder associated with aberrant expression of a polypeptideof interest in an animal, preferably a mammal and most preferably ahuman. In one embodiment, diagnosis comprises: (a) administering (forexample, parenterally, subcutaneously, or intraperitoneally) to asubject an effective amount of a labeled molecule which specificallybinds to the polypeptide of interest; (b) waiting for a time intervalfollowing the administering for permitting the labeled molecule topreferentially concentrate at sites in the subject where the polypeptideis expressed (and for unbound labeled molecule to be cleared tobackground level); (c) determining background level; and (d) detectingthe labeled molecule in the subject, such that detection of labeledmolecule above the background level indicates that the subject has aparticular disease or disorder associated with aberrant expression ofthe polypeptide of interest. Background level can be determined byvarious methods including, comparing the amount of labeled moleculedetected to a standard value previously determined for a particularsystem. As described herein, specific embodiments of the invention aredirected to the use of the antibodies of the invention to quantitate orqualitate concentrations of cells of B cell lineage or cells ofmonocytic lineage.

Also as described herein, antibodies of the invention may be used totreat, diagnose, or prognose an individual having an immunodeficiency.In a specific embodiment, antibodies of the invention are used to treat,diagnose, and/or prognose an individual having common variableimmunodeficiency disease (CVID) or a subset of this disease. In anotherembodiment, antibodies of the invention are used to diagnose, prognose,treat or prevent a disorder characterized by deficient serumimmunoglobulin production, recurrent infections, and/or immune systemdysfunction.

Also as described herein, antibodies of the invention may be used totreat, diagnose, or prognose an individual having an autoimmune diseaseor disorder. In a specific embodiment, antibodies of the invention areused to treat, diagnose, and/or prognose an individual having systemiclupus erythematosus, or a subset of the disease. In another specificembodiment, antibodies of the invention are used to treat, diagnoseand/or prognose an individual having rheumatoid arthritis, or a subsetof this disease.

It will be understood in the art that the size of the subject and theimaging system used will determine the quantity of imaging moiety neededto produce diagnostic images. In the case of a radioisotope moiety, fora human subject, the quantity of radioactivity injected will normallyrange from about 5 to 20 millicuries of ^(99m)Tc. The labeled antibodyor antibody fragment will then preferentially accumulate at the locationof cells which contain the specific protein. In vivo tumor imaging isdescribed in S. W. Burchiel et al., “Immunopharmacokinetics ofRadiolabeled Antibodies and Their Fragments.” (Chapter 13 in TumorImaging The Radiochemical Detection of Cancer, S. W. Burchiel and B. A.Rhodes, eds., Masson Publishing Inc. (1982).

Depending on several variables, including the type of label used and themode of administration, the time interval following the administrationfor permitting the labeled molecule to preferentially concentrate atsites in the subject and for unbound labeled molecule to be cleared tobackground level is 6 to 48 hours or 6 to 24 hours or 6 to 12 hours. Inanother embodiment the time interval following administration is 5 to 20days or 5 to 10 days.

In an embodiment, monitoring of the disease or disorder is carried outby repeating the method for diagnosing the disease or disease, forexample, one month after initial diagnosis, six months after initialdiagnosis, one year after initial diagnosis, etc.

Presence of the labeled molecule can be detected in the patient usingmethods known in the art for in vivo scanning. These methods depend uponthe type of label used. Skilled artisans will be able to determine theappropriate method for detecting a particular label. Methods and devicesthat may be used in the diagnostic methods of the invention include, butare not limited to, computed tomography (CT), whole body scan such asposition emission tomography (PET), magnetic resonance imaging (MRI),and sonography.

In a specific embodiment, the molecule is labeled with a radioisotopeand is detected in the patient using a radiation responsive surgicalinstrument (Thurston et al., U.S. Pat. No. 5,441,050). In anotherembodiment, the molecule is labeled with a fluorescent compound and isdetected in the patient using a fluorescence responsive scanninginstrument. In another embodiment, the molecule is labeled with apositron emitting metal and is detected in the patent using positronemission-tomography. In yet another embodiment, the molecule is labeledwith a paramagnetic label and is detected in a patient using magneticresonance imaging (MRI).

Kits

The present invention provides kits that can be used in the abovemethods. In one embodiment, a kit comprises an antibody of theinvention, preferably a purified antibody, in one or more containers. Ina specific embodiment, the kits of the present invention contain asubstantially isolated polypeptide comprising an epitope which isspecifically immunoreactive with an antibody included in the kit.Preferably, the kits of the present invention further comprise a controlantibody which does not react with the polypeptide of interest. Inanother specific embodiment, the kits of the present invention comprisetwo or more antibodies (monoclonal and/or polyclonal) that recognize thesame and/or different sequences or regions of the polypeptide of theinvention. In another specific embodiment, the kits of the presentinvention contain a means for detecting the binding of an antibody to apolypeptide of interest (e.g., the antibody may be conjugated to adetectable substrate such as a fluorescent compound, an enzymaticsubstrate, a radioactive compound or a luminescent compound, or a secondantibody which recognizes the first antibody may be conjugated to adetectable substrate).

In another specific embodiment of the present invention, the kit is adiagnostic kit for use in screening serum containing antibodies specificagainst proliferative and/or cancerous polynucleotides and polypeptides.Such a kit may include a control antibody that does not react with thepolypeptide of interest. Such a kit may include a substantially isolatedpolypeptide antigen comprising an epitope which is specificallyimmunoreactive with at least one anti-polypeptide antigen antibody.Further, such a kit includes means for detecting the binding of saidantibody to the antigen (e.g., the antibody may be conjugated to afluorescent compound such as fluorescein or rhodamine which can bedetected by flow cytometry). In specific embodiments, the kit mayinclude a recombinantly produced or chemically synthesized polypeptideantigen. The polypeptide antigen of the kit may also be attached to asolid support.

In a more specific embodiment the detecting means of the above-describedkit includes a solid support to which said polypeptide antigen isattached. Such a kit may also include a non-attached reporter-labeledanti-human antibody. In this embodiment, binding of the antibody to thepolypeptide antigen can be detected by binding of the saidreporter-labeled antibody.

In an additional embodiment, the invention includes a diagnostic kit foruse in screening serum containing antigens of the polypeptide of theinvention. The diagnostic kit includes a substantially isolated antibodyspecifically immunoreactive with polypeptide or polynucleotide antigens,and means for detecting the binding of the polynucleotide or polypeptideantigen to the antibody. In one embodiment, the antibody is attached toa solid support. In a specific embodiment, the antibody may be amonoclonal antibody. The detecting means of the kit may include asecond, labeled monoclonal antibody. Alternatively, or in addition, thedetecting means may include a labeled, competing antigen.

In one diagnostic configuration, test serum is reacted with a solidphase reagent having a surface-bound antigen obtained by the methods ofthe present invention. After binding with specific antigen antibody tothe reagent and removing unbound serum components by washing, thereagent is reacted with reporter-labeled anti-human antibody to bindreporter to the reagent in proportion to the amount of boundanti-antigen antibody on the solid support. The reagent is again washedto remove unbound labeled antibody, and the amount of reporterassociated with the reagent is determined. Typically, the reporter is anenzyme which is detected by incubating the solid phase in the presenceof a suitable fluorometric, luminescent or colorimetric substrate(Sigma, St. Louis, Mo.).

The solid surface reagent in the above assay is prepared by knowntechniques for attaching protein material to solid support material,such as polymeric beads, dip sticks, 96-well plate or filter material.These attachment methods generally include non-specific adsorption ofthe protein to the support or covalent attachment of the protein,typically through a free amine group, to a chemically reactive group onthe solid support, such as an activated carboxyl, hydroxyl, or aldehydegroup. Alternatively, streptavidin coated plates can be used inconjunction with biotinylated antigen(s).

Thus, the invention provides an assay system or kit for carrying outthis diagnostic method. The kit generally includes a support withsurface-bound recombinant antigens, and a reporter-labeled anti-humanantibody for detecting surface-bound anti-antigen antibody.

The invention further relates to antibodies which act as agonists orantagonists of the polypeptides of the present invention. For example,the present invention includes antibodies which disrupt thereceptor/ligand interactions with the polypeptides of the inventioneither partially or fully. Included are both receptor-specificantibodies and ligand-specific antibodies. Included arereceptor-specific antibodies which do not prevent ligand binding butprevent receptor activation. Receptor activation (i.e., signaling) maybe determined by techniques described herein or otherwise known in theart. Also included are receptor-specific antibodies which both preventligand binding and receptor activation. Likewise, included areneutralizing antibodies which bind the ligand and prevent binding of theligand to the receptor, as well as antibodies which bind the ligand,thereby preventing receptor activation, but do not prevent the ligandfrom binding the receptor. Further included are antibodies whichactivate the receptor. These antibodies may act as agonists for eitherall or less than all of the biological activities affected byligand-mediated receptor activation. The antibodies may be specified asagonists or antagonists for biological activities comprising specificactivities disclosed herein. Further included are antibodies that bindto Neutrokine-alpha and/or Neutrokine-alphaSV irrespective of whetherNeutrokine-alpha or Neutrokine-alphaSV is bound to a Neutrokine-alphaReceptor. These antibodies act as Neutrokine-alpha and/orNeutrokine-alphaSV agonists as reflected in an increase in cellularproliferation in response to binding of Neutrokine-alpha and/orNeutrokine-alphaSV to a Neutrokine-alpha receptor in the presence ofthese antibodies. The above antibody agonists can be made using methodsknown in the art. See e.g., WO 96/40281; U.S. Pat. No. 5,811,097; Deng,B. et al., Blood 92(6):1981-1988 (1998); Chen, Z. et al., Cancer Res.58(16):3668-3678 (1998); Harrop, J. A. et al., J. Immunol.161(4):1786-1794 (1998); Zhu, Z. et al., Cancer Res. 58(15):3209-3214(1998); Yoon, D. Y. et al., J. Immunol. 160(7):3170-3179 (1998); Prat,M. et al., J. Cell. Sci. 111(Pt2):237-247 (1998); Pitard, V. et al., J.Immunol. Methods 205(2):177-190 (1997); Liautard, J. et al., Cytokinde9(4):233-241 (1997); Carlson, N. G. et al., J. Biol. Chem.272(17):11295-11301 (1997); Taryman, R. E. et al., Neuron 14(4):755-762(1995); Muller, Y. A. et al., Structure 6(9):1153-1167 (1998); Bartunek,P. et al., Cytokine 8(1):14-20 (1996) (said references incorporated byreference in their entireties).

At least fourteen monoclonal antibodies have been generated againstNeutrokine-alpha. These monoclonal antibodies are designated: 12D6, 2E5,9B6, 1B8, 5F4, 9A5, 10G12, 11G12, 16B4, 3D4, 16C9, 13D5, 15C10, and12C5. Preliminary analysis of these antibodies indicates that each bindsNeutrokine-alpha protein in a Western blot analysis and whenNeutrokine-alpha protein is bound to an ELISA plate. However, furtheranalysis of antibodies 12D6, 2E5, 9B6, 1B8, 5F4, 9A5, 10G12, 11G12, and16B4 indicates that only the antibodies designated 12D6, 9B6, 2E5,10G12, 9A5, and 11G12 bind a membrane-bound form of Neutrokine-alpha.Thus, a subset of the monoclonal antibodies generated againstNeutrokine-alpha have been determined to bind only the membrane-boundform of Neutrokine-alpha (i.e., this subset does not bind the solubleform of Neutrokine-alpha corresponding to amino acids 134 to 285 of SEQID NO:2), which as discussed herein, is primarily limited to expressionon monocytes and dendritic cells.

Antibody 9B6 has been found to bind specifically to the membrane—boundform of Neutrokine-alpha, but not to the soluble form ofNeutrokine-alpha.

Epitope mapping of antibody 9B6 has indicated that this antibody bindsspecifically to an amino acid sequence contained in amino acid residuesfrom about Ser-171 to about Phe-194 of SEQ ID NO:2. More particularly,epitope mapping has indicated that antibody 9B6 binds specifically to apeptide comprising amino acid residues Lys-173 to Lys-188 of SEQ IDNO:2.

In contrast, antibodies 16C9 and 15C10 have been found to bind thesoluble form of Neutrokine-alpha (amino acids 134 to 285 of SEQ ID NO:2)and to inhibit Neutrokine-alpha-mediated proliferation of B cells. Seefor example, Example 10. The 15C10 antibody has also been found toinhibit binding of Neutrokine-alpha to its receptor. Epitope mapping ofantibody 15C10 has indicated that this antibody binds specifically to anamino acid sequence contained in amino acid residues from about Glu-223to about Tyr-246 of SEQ ID NO:2. More particularly, epitope mapping hasindicated that antibody 15C10 binds specifically to a peptide comprisingamino acid residues Val-227 to Asn-242 of SEQ ID NO:2. Antibody 15C10also binds specifically to a peptide comprising amino acid residuesPhe-230 to Cys-245 of SEQ ID NO:2.

As described above, anti-Neutrokine-alpha monoclonal antibodies havebeen prepared. Hybridomas producing the antibodies referred to as 9B6and 15C10 have been deposited with the ATCC and have been assigneddeposit accession numbers PTA-1158 and PTA-1159, respectively. In oneembodiment, the antibodies of the invention have one or more of the samebiological characteristics as one or more of the antibodies secreted bythe hybridoma cell lines deposited under accession numbers PTA-1158 orPTA-1159. By “biological characteristics” is meant, the in vitro or invivo activities or properties of the antibodies, such as, for example,the ability to bind to Neutrokine-alpha (e.g., the polypeptide of SEQ IDNO:2, the mature form of Neutrokine-alpha, the membrane-bound form ofNeutrokine-alpha, the soluble form of Neutrokine-alpha (amino acids 134to 285 of SEQ ID NO:2), and an antigenic and/or epitope region ofNeutrokine-alpha), the ability to substantially blockNeutrokine-alpha/Neutrokine-alpha receptor binding, or the ability toblock Neutrokine-alpha mediated biological activity (e.g., stimulationof B cell proliferation and immunoglobulin production). Optionally, theantibodies of the invention will bind to the same epitope as at leastone of the antibodies specifically referred to herein. Such epitopebinding can be routinely determined using assays known in the art.

Thus, in one embodiment, the invention provides antibodies thatspecifically bind the membrane-bound form of Neutrokine-alpha and do notbind the soluble form of Neutrokine-alpha. These antibodies have useswhich include, but are not limited to, as diagnostic probes foridentifying and/or isolating monocyte lineages expressing the membranebound form of Neutrokine-alpha. For example, the expression of themembrane bound form of Neutrokine-alpha is elevated on activatedmonocytes, and accordingly, antibodies encompassed by the invention maybe used to detect and/or quantitate levels of activated monocytes.Additionally, antibodies that only bind the membrane bound form ofNeutrokine-alpha may be used to target toxins to neoplastic,preneoplastic, and/or other cells that express the membrane bound formof Neutrokine-alpha (e.g., monocytes and dendritic cells).

In another embodiment, antibodies of the invention specifically bindonly the soluble form of Neutrokine-alpha (amino acids 134 to 285 of SEQID NO:2). These antibodies have uses which include, but are not limitedto, uses such as diagnostic probes for assaying soluble Neutrokine-alphain biological samples, and as therapeutic agents that target toxins tocells expressing Neutrokine-alpha receptors (e.g., B cells), and/or toreduce or block in vitro or in vivo Neutrokine-alpha mediated biologicalactivity (e.g., stimulation of B cell proliferation and/orimmunoglobulin production).

The invention also provides for antibodies that specifically bind boththe membrane-bound and soluble form of Neutrokine-alpha.

As described above, the invention encompasses antibodies that inhibit orreduce the ability of Neutrokine-alpha and/or Neutrokine-alphaSV to bindNeutrokine-alpha receptor and/or Neutrokine-alphaSV receptor in vitroand/or in vivo. In a specific embodiment, antibodies of the inventioninhibit or reduce the ability of Neutrokine-alpha and/orNeutrokine-alphaSV to bind Neutrokine-alpha receptor and/orNeutrokine-alphaSV receptor in vitro. In another nonexclusive specificembodiment, antibodies of the invention inhibit or reduce the ability ofNeutrokine-alpha and/or Neutrokine-alphaSV to bind Neutrokine-alphareceptor and/or Neutrokine-alphaSV receptor in vivo. Such inhibition canbe assayed using techniques described herein or otherwise known in theart.

The invention also encompasses, antibodies that bind specifically toNeutrokine-alpha and/or Neutrokine-alphaSV, but do not inhibit theability of Neutrokine-alpha and/or Neutrokine-alphaSV to bindNeutrokine-alpha receptor and/or Neutrokine-alphaSV receptor in vitroand/or in vivo. In a specific embodiment, antibodies of the invention donot inhibit or reduce the ability of Neutrokine-alpha and/orNeutrokine-alphaSV to bind Neutrokine-alpha receptor and/orNeutrokine-alphaSV receptor in vitro. In another nonexclusive specificembodiment, antibodies of the invention do not inhibit or reduce theability of Neutrokine-alpha and/or Neutrokine-alphaSV to bindNeutrokine-alpha receptor and/or Neutrokine-alphaSV receptor in vivo.

As described above, the invention encompasses antibodies that inhibit orreduce a Neutrokine-alpha and/or Neutrokine-alphaSV-mediated biologicalactivity in vitro and/or in vivo. In a specific embodiment, antibodiesof the invention inhibit or reduce Neutrokine-alpha- and/orNeutrokine-alphaSV-mediated B cell proliferation in vitro. Suchinhibition can be assayed by routinely modifying B cell proliferationassays described herein or otherwise known in the art. In anothernonexclusive specific embodiment, antibodies of the invention inhibit orreduce Neutrokine-alpha- and/or Neutrokine-alphaSV-mediated B cellproliferation in vivo. In a specific embodiment, the antibody of theinvention is 15C10, or a humanized form thereof. In another preferredspecific embodiment, the antibody is 16C9, or a humanized form thereof.Thus, in specific embodiments of the invention, a 16C9 and/or 15C10antibody, or humanized forms thereof, are used to bind solubleNeutrokine-alpha and/or Neutrokine-alphaSV and/or agonists and/orantagonists thereof and thereby inhibit (either partially or completely)B cell proliferation.

Alternatively, the invention also encompasses, antibodies that bindspecifically to a Neutrokine-alpha and/or Neutrokine-alphaSV, but do notinhibit or reduce a Neutrokine-alpha and/or Neutrokine-alphaSV-mediatedbiological activity in vitro and/or in vivo (e.g., stimulation of B cellproliferation). In a specific embodiment, antibodies of the invention donot inhibit or reduce a Neutrokine-alpha and/orNeutrokine-alphaSV-mediated biological activity in vitro. In anothernon-exclusive embodiment, antibodies of the invention do not inhibit orreduce a Neutrokine-alpha and/or Neutrokine-alphaSV mediated biologicalactivity in vivo. In a specific embodiment, the antibody of theinvention is 9B6, or a humanized form thereof.

As described above, the invention encompasses antibodies thatspecifically bind to the same epitope as at least one of the antibodiesspecifically referred to herein, in vitro and/or in vivo.

In a specific embodiment, the antibodies of the invention specificallybind to an amino acid sequence contained in amino acid residues fromabout Ser-171 to about Phe-194 of SEQ ID NO:2, in vitro. In anotherspecific, non-exclusive embodiment, the antibodies of the inventionspecifically bind to an amino acid sequence contained in amino acidresidues from about Ser-171 to about Phe-194 of SEQ ID NO:2, in vivo. Inanother specific, non-exclusive embodiment, the antibodies of theinvention specifically bind to an amino acid sequence contained in aminoacid residues from Lys-173 to Lys-188 of SEQ ID NO:2, in vitro. Inanother specific, non-exclusive embodiment, the antibodies of theinvention specifically bind to an amino acid sequence contained in aminoacid residues from Lys-173 to Lys-188 of SEQ ID NO:2, in vivo.

In an additional specific embodiment, the antibodies of the inventionspecifically bind to an amino acid sequence contained in amino acidresidues from about Glu-223 to about Tyr-246 of SEQ ID NO:2, in vitro.In another specific, non-exclusive embodiment, the antibodies of theinvention specifically bind to an amino acid sequence contained in aminoacid residues from about Glu-223 to about Tyr-246 of SEQ ID NO:2, invivo. In another specific, non-exclusive embodiment, the antibodies ofthe invention specifically bind to an amino acid sequence contained inamino acid residues from Val-227 to Asn-242 of SEQ ID NO:2, in vitro. Inanother specific, non-exclusive embodiment, the antibodies of theinvention specifically bind to an amino acid sequence contained in aminoacid residues from Val-227 to Asn-242 of SEQ ID NO:2, in vivo. Inanother specific, non-exclusive embodiment, the antibodies of theinvention specifically bind to an amino acid sequence contained in aminoacid residues from Phe-230 to Cys-245 of SEQ ID NO:2, in vitro. Inanother specific, non-exclusive embodiment, the antibodies of theinvention specifically bind to an amino acid sequence contained in aminoacid residues from Phe-230 to Cys-245 of SEQ ID NO:2, in vivo.

The invention also provides antibodies that competitively inhibit thebinding of the 9B6 monoclonal antibody produced by the hybridomadeposited as PTA-1159 to a polypeptide of the invention, preferably thepolypeptide of SEQ ID NO:2, more preferably to a polypeptide having theamino acid sequence of residues Ser-171 to Phe-194 of SEQ ID NO:2.Competitive inhibition can be determined by any method known in the art,for example, using the competitive binding assays described herein. Inpreferred embodiments, the antibody competitively inhibits the bindingof 9B6 monoclonal antibody by at least 95%, at least 90%, at least 85%,at least 80%, at least 75%, at least 70%, at least 60%, at least 50%, tothe polypeptide of SEQ ID NO:2, or more preferably to a polypeptidehaving the amino acid sequence of residues Ser-171 to Phe-194 of SEQ IDNO:2.

The invention also provides antibodies that competitively inhibit thebinding of the 15C10 monoclonal antibody produced by the hybridomadeposited as PTA-1158 to a polypeptide of the invention, preferably thepolypeptide of SEQ ID NO:2, more preferably to a polypeptide having theamino acid sequence of residues Glu-223 to Tyr-246 of SEQ ID NO:2. Inpreferred embodiments, the antibody competitively inhibits the bindingof 15C10 monoclonal antibody by at least 95%, at least 90%, at least85%, at least 80%, at least 75%, at least 70%, at least 60%, at least50%, to the polypeptide of SEQ ID NO:2, or more preferably to apolypeptide having the amino acid sequence of residues Glu-223 toTyr-246 of SEQ ID NO:2.

Additional embodiments of the invention are directed to the 9B6 antibodyand to the hybridoma cell line expressing this antibody. A hybridomacell line expressing Antibody 9B6 was deposited with the ATCC on Jan. 7,2000 and has been assigned ATCC Deposit No. PTA-1159. In a preferredembodiment, antibody 9B6 is humanized.

Additional embodiments of the invention are directed to the 15C10antibody and to the hybridoma cell line expressing this antibody. Ahybridoma cell line expressing Antibody 15C10 was deposited with theATCC on Jan. 7, 2000 and has been assigned ATCC Deposit No. PTA-1158. Ina preferred embodiment, antibody 15C10 is humanized.

In a specific embodiment, the specific antibodies described above arehumanized using techniques described herein or otherwise known in theart and then used as therapeutics as described herein.

In another specific embodiment, any of the antibodies listed above areused in a soluble form.

In another specific embodiment, any of the antibodies listed above areconjugated to a toxin or a label (as described infra). Such conjugatedantibodies are used to kill a particular population of cells or toquantitate a particular population of cells. In a preferred embodiment,such conjugated antibodies are used to kill B cells expressingNeutrokine-alpha receptor on their surface. In another preferredembodiment, such conjugated antibodies are used to quantitate B cellsexpressing Neutrokine-alpha receptor on their surface.

In another specific embodiment, any of the antibodies listed above areconjugated to a toxin or a label (as described infra). Such conjugatedantibodies are used to kill a particular population of cells or toquantitate a particular population of cells. In a preferred embodiment,such conjugated antibodies are used to kill monocyte cells expressingthe membrane-bound form of Neutrokine-alpha. In another preferredembodiment, such conjugated antibodies are used to quantitate monocytecells expressing the membrane-bound form of Neutrokine-alpha.

The antibodies of the invention also have uses as therapeutics and/orprophylactics which include, but are not limited to, in activatingmonocytes or blocking monocyte activation and/or killing monocytelineages that express the membrane bound form of Neutrokine-alpha ontheir cell surfaces (e.g., to treat, prevent, and/or diagnose myeloidleukemias, monocyte based leukemias and lymphomas, monocytosis,monocytopenia, rheumatoid arthritis, and other diseases or conditionsassociated with activated monocytes). In a specific embodiment, theantibodies of the invention fix complement. In other specificembodiments, as further described herein, the antibodies of theinvention (or fragments thereof) are associated with heterologouspolypeptides or nucleic acids (e.g., toxins, such as, compounds thatbind and activate endogenous cytotoxic effecter systems, andradioisotopes; and cytotoxic prodrugs).

In another embodiment, one or more monoclonal antibodies are producedwherein they recognize or bind Neutrokine-alpha and/or a mutein thereof,but do not recognize or bind Neutrokine-alphaSV and/or a mutein thereof.In a related embodiment, one or more monoclonal antibodies are producedwherein they recognize or bind Neutrokine-alphaSV and/or a muteinthereof, but do not recognize or bind Neutrokine-alpha and/or a muteinthereof.

As discussed above, antibodies to the Neutrokine-alpha and/orNeutrokine-alpha SV polypeptides of the invention can, in turn, beutilized to generate anti-idiotype antibodies that “mimic” theNeutrokine-alpha, using techniques well known to those skilled in theart. (See, e.g., Greenspan & Bona, FASEB J. 7(5):437-444 (1989), andNissinoff, J. Immunol. 147(8):2429-2438 (1991)). For example, antibodieswhich bind to Neutrokine-alpha and/or Neutrokine-alpha SV andcompetitively inhibit the Neutrokine-alpha and/or Neutrokine-alpha SVmultimerization and/or binding to ligand can be used to generateanti-idiotypes that “mimic” the Neutrokine-alpha TNF multimerizationand/or binding domain and, as a consequence, bind to and neutralizeNeutrokine-alpha or Neutrokine-alpha SV and/or its ligand. Suchneutralizing anti-idiotypes or Fab fragments of such anti-idiotypes canbe used in therapeutic regimens to neutralize Neutrokine-alpha ligand.For example, such anti-idiotypic antibodies can be used to bindNeutrokine-alpha and/or Neutrokine-alpha SV, or to bind Neutrokine-alphaand/or Neutrokine-alpha SV receptors on the surface of cells of B celllineage, and thereby block Neutrokine-alpha and/or Neutrokine-alpha SVmediated B cell activation, proliferation, and/or differentiation.

Immune System-Related Disorder Diagnosis

Neutrokine-alpha is expressed in kidney, lung, peripheral leukocyte,bone marrow, T cell lymphoma, B cell lymphoma, activated T cells,stomach cancer, smooth muscle, macrophages, and cord blood tissue, andparticularly cells of monocytic lineage. Moreover, Neutrokine-alphaSV isexpressed in primary dendritic cells. Additionally, Neutrokine-alpha isexpressed on the cell surface of the following non-hematopoietic tumorcell lines. Colon carcinomas HCT 116 (ATCC Accession No. CCL-247) andHT-29 (ATCC Accession No. HTB-38); Colon adenocarcinomas Caco-2 (ATCCAccession No. HTB-37), COLO 201 (ATCC Accession No. CCL-224), and WiDr(ATCC Accession No. CCL-218); Breast adenocarcinoma MDA-MB-231 (ATCCAccession No. HTB-26); Bladder squamous carcinoma SCaBER (ATCC AccessionNo. HTB-3); Bladder carcinoma HT-1197 (ATCC Accession No. CRL-1473);Kidney carcinomas A-498 (ATCC Accession No. HTB-44), Caki-1 (ATCCAccession No. HTB-46), and Caki-2 (ATCC Accession No. HTG-47); Kidney,Wilms tumor SK-NEP-1 (ATCC Accession No. HTB-48); and Pancreascarcinomas Hs 766T (ATCC Accession No. HTB-134), MIA PaCa-2 (ATCCAccession No. CRL-1420), and SU.86.86 (ATCC Accession No. CRL-1837). Fora number of immune system-related disorders, substantially altered(increased or decreased) levels of Neutrokine-alpha and/orNeutrokine-alphaSV gene expression can be detected in immune systemtissue or other cells or bodily fluids (e.g., sera, plasma, urine,synovial fluid or spinal fluid) taken from an individual having such adisorder, relative to a “standard” Neutrokine-alpha and/orNeutrokine-alphaSV gene expression level, that is, the Neutrokine-alphaand/or Neutrokine-alphaSV expression level in immune system tissues orbodily fluids from an individual not having the immune system disorder.Thus, the invention provides a diagnostic method useful during diagnosisof an immune system disorder, which involves measuring the expressionlevel of the gene encoding the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide in immune system tissue or other cells orbody fluid from an individual and comparing the measured gene expressionlevel with a standard Neutrokine-alpha and/or Neutrokine-alphaSV geneexpression level, whereby an increase or decrease in the gene expressionlevel compared to the standard is indicative of an immune systemdisorder or normal activation, proliferation, differentiation, and/ordeath.

In particular, it is believed that certain tissues in mammals withcancer of cells or tissue of the immune system express significantlyenhanced or reduced levels of the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide and mRNA encoding the Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide when compared to a corresponding“standard” level. Further, it is believed that enhanced or depressedlevels of the Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide canbe detected in certain body fluids (e.g., sera, plasma, urine, andspinal fluid) or cells or tissue from mammals with such a cancer whencompared to sera from mammals of the same species not having the cancer.

For example, as disclosed herein, Neutrokine-alpha is highly expressedin cells of monocytic lineage. Accordingly, polynucleotides of theinvention (e.g., polynucleotide sequences complementary to all or aportion of Neutrokine-alpha mRNA and/or Neutrokine-alphaSV mRNA) andantibodies (and antibody fragments) directed against the polypeptides ofthe invention may be used to quantitate or qualitate concentrations ofcells of monocytic lineage (e.g., monocytic leukemia cells) expressingNeutrokine-alpha on their cell surfaces. These antibodies additionallyhave diagnostic applications in detecting abnormalities in the level ofNeutrokine-alpha gene expression, or abnormalities in the structureand/or temporal, tissue, cellular, or subcellular location ofNeutrokine-alpha and/or Neutrokine-alphaSV. These diagnostic assays maybe performed in vivo or in vitro, such as, for example, on bloodsamples, biopsy tissue or autopsy tissue.

Additionally, as disclosed herein, Neutrokine-alpha receptor isexpressed primarily on cells of B cell lineage. Accordingly,Neutrokine-alpha polypeptides of the invention (including labeledNeutrokine-alpha polypeptides and Neutrokine-alpha fusion proteins), andanti-Neutrokine-alpha antibodies (including anti-Neutrokine-alphaantibody fragments) against the polypeptides of the invention may beused to quantitate or qualitate concentrations of cells of B celllineage (e.g., B cell related leukemias or lymphomas) expressingNeutrokine-alpha receptor on their cell surfaces. These Neutrokine-alphapolypeptides and antibodies additionally have diagnostic applications indetecting abnormalities in the level of Neutrokine-alpha receptor geneexpression, or abnormalities in the structure and/or temporal, tissue,cellular, or subcellular location of Neutrokine-alpha receptor and/ordiagnosing activity/defects in signalling pathways associated withNeutrokine-alpha. These diagnostic assays may be performed in vivo or invitro, such as, for example, on blood samples or biopsy tissue usingtechniques described herein or otherwise known in the art.

In one embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides or Neutrokine-alpha and/orNeutrokine-alphaSV agonists or antagonists (e.g., anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibodies) of the invention are used totreat, prevent, diagnose, or prognose an individual having animmunodeficiency.

Immunodeficiencies that may be treated, prevented, diagnosed, and/orprognosed with the Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides or Neutrokine-alpha and/orNeutrokine-alphaSV agonists or antagonists (e.g., anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibodies) of the invention, include,but are not limited to one or more immunodeficiencies selected from:severe combined immunodeficiency (SCID)-X linked, SCID-autosomal,adenosine deaminase deficiency (ADA deficiency), X-linkedagammaglobulinemia (XLA), Bruton's disease, congenitalagammaglobulinemia, X-linked infantile agammaglobulinemia, acquiredagammaglobulinemia, adult onset agammaglobulinemia, late-onsetagammaglobulinemia, dysgammaglobulinemia, hypogammaglobulinemia,transient hypogammaglobulinemia of infancy, unspecifiedhypogammaglobulinemia, agammaglobulinemia, common variableimmunodeficiency (CVID) (acquired), Wiskott-Aldrich Syndrome (WAS),X-linked immunodeficiency with hyper IgM, non X-linked immunodeficiencywith hyper IgM, selective IgA deficiency, IgG subclass deficiency (withor without IgA deficiency), antibody deficiency with normal or elevatedIgs, immunodeficiency with thymoma, Ig heavy chain deletions, kappachain deficiency, B cell lymphoproliferative disorder (BLPD), selectiveIgM immunodeficiency, recessive agammaglobulinemia (Swiss type),reticular dysgenesis, neonatal neutropenia, severe congenitalleukopenia, thymic alymphoplasia-aplasia or dysplasia withimmunodeficiency, ataxia-telangiectasia, short limbed dwarfism, X-linkedlymphoproliferative syndrome (XLP), Nezelof syndrome-combinedimmunodeficiency with Igs, purine nucleoside phosphorylase deficiency(PNP), MHC Class II deficiency (Bare Lymphocyte Syndrome) and severecombined immunodeficiency.

According to this embodiment, an individual having an immunodeficiencyexpresses aberrantly low levels of Neutrokine-alpha and/orNeutrokine-alpha SV when compared to an individual not having animmunodeficiency. Any means described herein or otherwise known in theart may be applied to detect Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides of the invention (e.g., FACS analysis orELISA detection of Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the invention and hybridization or PCR detection ofNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides of theinvention) and to determine the expression profile of Neutrokine-alphaand/or Neutrokine-alphaSV polynucleotides and/or polypeptides of theinvention in a biological sample.

A biological sample of a person afflicted with an immunodeficiency ischaracterized by low levels of expression of Neutrokine-alpha and/orNeutrokine-alphaSV when compared to that observed in individuals nothaving an immunodeficiency. Thus, Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides and/or polypeptides of the invention,and/or agonists or antagonists thereof, may be used according to themethods of the invention in the diagnosis and/or prognosis of animmunodeficiency. For example, a biological sample obtained from aperson suspected of being afflicted with an immunodeficiency (“thesubject”) may be analyzed for the relative expression level(s) ofNeutrokine-alpha, and/or Neutrokine-alphaSV polynucleotides and/orpolypeptides of the invention. The expression level(s) of one or more ofthese molecules of the invention is (are) then compared to theexpression level(s) of the same molecules of the invention as expressedin a person known not to be afflicted with an immunodeficiency. Asignificant difference in expression level(s) of Neutrokine-alpha,and/or Neutrokine-alphaSV, polynucleotides and/or polypeptides of theinvention, and/or agonists and/or antagonists thereof, between samplesobtained from the subject and the control suggests that the subject isafflicted with an immunodeficiency.

In another embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides or Neutrokine-alpha and/orNeutrokine-alphaSV agonists or antagonists (e.g., anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibodies) of the invention are used totreat, diagnose and/or prognose an individual having common variableimmunodeficiency disease (“CVID”; also known as “acquiredagammaglobulinemia” and “acquired hypogammaglobulinemia”) or a subset ofthis disease. According to this embodiment, an individual having CVID ora subset of individuals having CVID expresses aberrant levels ofNeutrokine-alpha and/or Neutrokine-alpha Receptor on their B cellsand/or monocytes, when compared to individuals not having CVID. Anymeans described herein or otherwise known in the art may be applied todetect Neutrokine-alpha polynucleotides or polypeptides of the inventionand/or Neutrokine-alpha Receptor polypeptides (e.g., FACS analysis orELISA detection of Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the invention and hybridization or PCR detection ofNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides of theinvention) and to determine differentially the expression profile ofNeutrokine-alpha, and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention and/or Neutrokine-alpha receptorpolypeptides in a sample containing at least monocyte cells or somecomponent thereof (e.g., RNA) as compared to a sample containing atleast B cells or a component thereof (e.g., RNA). In the instance wherea sample containing at least monocyte cells or some component thereof(e.g., RNA) is determined to reflect Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotide or polypeptide expression and a samplecontaining at least B cells or a component thereof (e.g., RNA) isdetermined to reflect less than normal levels of Neutrokine-alphareceptor polynucleotide or polypeptide expression, the samples may becorrelated with the occurrence of CVID (i.e., “acquiredagammaglobulinemia” or “acquired hypogammaglobulinemia”).

A subset of persons afflicted with CVID are characterized by high levelsof expression of both Neutrokine-alpha and the Neutrokine-alpha receptor(“NAR”) in peripheral or circulating B cells when compared to thatobserved in individuals not having CVID. In contrast, persons who arenot afflicted with CVID are typically characterized by low levels ofNeutrokine-alpha expression and high levels of NAR expression inperipheral or circulating B cells. Thus, Neutrokine-alpha,Neutrokine-alphaSV polypeptides, and/or NAR polypeptides,polynucleotides and/or polypeptides of the invention, and/or agonists orantagonists thereof, may be used according to the methods of theinvention in the differential diagnosis of this subset of CVID. Forexample, a sample of peripheral B cells obtained from a person suspectedof being afflicted with CVID (“the subject”) may be analyzed for therelative expression level(s) of Neutrokine-alpha, Neutrokine-alphaSV,and/or NAR polynucleotides and/or polypeptides of the invention. Theexpression level(s) of one or more of these molecules of the inventionis (are) then compared to the expression level(s) of the same moleculesof the invention as expressed in a person known not to be afflicted withCVID (“the control”). A significant difference in expression level(s) ofNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention, and/or NAR polypeptides, and/or agonistsand/or antagonists thereof, between samples obtained from the subjectand the control suggests that the subject is afflicted with this subsetof CVID.

In a specific embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides, or agonists or antagonists thereof(e.g., anti-Neutrokine-alpha, and/or anti-Neutrokine-alphaSV,antibodies) are used to diagnose, prognose, treat, or prevent a disordercharacterized by deficient serum immunoglobulin production, recurrentinfections, and/or immune system dysfunction. Moreover,Neutrokine-alpha, and/or Neutrokine-alphaSV polynucleotides orpolypeptides, or agonists or antagonists thereof (e.g.,anti-Neutrokine-alpha and/or anti-Neutrokine-alphaSV antibodies) may beused to diagnose, prognose, treat, or prevent infections of the joints,bones, skin, and/or parotid glands, blood-borne infections (e.g.,sepsis, meningitis, septic arthritis, and/or osteomyelitis), autoimmunediseases (e.g., those disclosed herein), inflammatory disorders, andmalignancies, and/or any disease or disorder or condition associatedwith these infections, diseases, disorders and/or malignancies)including, but not limited to, CVID, other primary immune deficiencies,HIV disease, CLL, recurrent bronchitis, sinusitis, otitis media,conjunctivitis, pneumonia, hepatitis, meningitis, herpes zoster (e.g.,severe herpes zoster), and/or pneumocystis carnii.

In another embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides or Neutrokine-alpha and/orNeutrokine-alphaSV agonists or antagonists (e.g., anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibodies) of the invention are used totreat, diagnose, or prognose an individual having an autoimmune diseaseor disorder.

Autoimmune diseases or disorders that may be treated, diagnosed, orprognosed using Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides or Neutrokine-alpha and/orNeutrokine-alphaSV agonists or antagonists (e.g., anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibodies) of the invention include, butare not limited to, one or more of the following: autoimmune hemolyticanemia, autoimmune neonatal thrombocytopenia, idiopathicthrombocytopenia purpura, autoimmunocytopenia, hemolytic anemia,antiphospholipid syndrome, dermatitis, allergic encephalomyelitis,myocarditis, relapsing polychondritis, rheumatic heart disease,glomerulonephritis (e.g., IgA nephropathy), Multiple Sclerosis,Neuritis, Uveitis Ophthalmia, Polyendocrinopathies, Purpura (e.g.,Henloch-Scoenlein purpura), Reiter's Disease, Stiff-Man Syndrome,Autoimmune Pulmonary Inflammation, Guillain-Barre Syndrome, insulindependent diabetes mellitus, and autoimmune inflammatory eye, autoimmunethyroiditis, hypothyroidism (i.e., Hashimoto's thyroiditis, systemiclupus erythematosus, Goodpasture's syndrome, Pemphigus, Receptorautoimmunities such as, for example, (a) Graves' Disease, (b) MyastheniaGravis, and (c) insulin resistance, autoimmune hemolytic anemia,autoimmune thrombocytopenic purpura, rheumatoid arthritis, schlerodermawith anti-collagen antibodies, mixed connective tissue disease,polymyositis/dermatomyositis, pernicious anemia, idiopathic Addison'sdisease, infertility, glomerulonephritis such as primaryglomerulonephritis and IgA nephropathy, bullous pemphigoid, Sjogren'ssyndrome, diabetes mellitus, and adrenergic drug resistance (includingadrenergic drug resistance with asthma or cystic fibrosis), chronicactive hepatitis, primary biliary cirrhosis, other endocrine glandfailure, vitiligo, vasculitis, post-MI, cardiotomy syndrome, urticaria,atopic dermatitis, asthma, inflammatory myopathies, and otherinflammatory, granulomatous, degenerative, and atrophic disorders.

According to this embodiment, an individual having an autoimmune diseaseor disorder expresses aberrantly high levels of Neutrokine-alpha,Neutrokine-alpha SV, and/or NAR when compared to an individual nothaving an autoimmune disease or disorder. Any means described herein orotherwise known in the art may be applied to detect Neutrokine-alpha,and/or Neutrokine-alphaSV polynucleotides or polypeptides of theinvention and/or NAR polypeptides (e.g., FACS analysis or ELISAdetection of Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides ofthe invention and hybridization or PCR detection of Neutrokine-alphaand/or Neutrokine-alphaSV polynucleotides of the invention) and todetermine the expression profile of Neutrokine-alpha and/orNeutrokine-alphaSV, polynucleotides and/or polypeptides of the inventionand/or NAR polypeptides in a biological sample.

A biological sample of persons afflicted with an autoimmune disease ordisorder is characterized by high levels of expression ofNeutrokine-alpha, Neutrokine-alphaSV, and/or NAR when compared to thatobserved in individuals not having an autoimmune disease or disorder.Thus, Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides and/orpolypeptides of the invention, and/or agonists or antagonists thereof,may be used according to the methods of the invention in the diagnosisand/or prognosis of an autoimmune disease or disorder. For example, abiological sample obtained from a person suspected of being afflictedwith an autoimmune disease or disorder (“the subject”) may be analyzedfor the relative expression level(s) of Neutrokine-alpha, and/orNeutrokine-alphaSV polynucleotides and/or polypeptides of the inventionand/or NAR polypeptides. The expression level(s) of one or more of thesemolecules of the invention is (are) then compared to the expressionlevel(s) of the same molecules of the invention as expressed in a personknown not to be afflicted with an autoimmune disease or disorder. Asignificant difference in expression level(s) of Neutrokine-alpha,and/or Neutrokine-alphaSV, polynucleotides and/or polypeptides of theinvention, and/or agonists and/or antagonists thereof, and/or NARpolypeptides between samples obtained from the subject and the controlsuggests that the subject is afflicted with an autoimmune disease ordisorder.

In another embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides or Neutrokine-alpha and/orNeutrokine-alphaSV agonists or antagonists (e.g., anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibodies) of the invention are used totreat, diagnose, or prognose an individual having systemic lupuserythematosus or a subset of this disease. According to this embodiment,an individual having systemic lupus erythematosus or a subset ofindividuals having systemic lupus erythematosus expresses aberrantlyhigh levels of Neutrokine-alpha and/or Neutrokine-alpha SV when comparedto an individual not having systemic lupus erythematosus or this subsetof systemic lupus erythematosus. Any means described herein or otherwiseknown in the art may be applied to detect Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides of the invention(e.g., FACS analysis or ELISA detection of Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention and hybridization orPCR detection of Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides of the invention) and to determine the expressionprofile of Neutrokine-alpha and/or Neutrokine-alphaSV, polynucleotidesand/or polypeptides of the invention in a biological sample.

A biological sample of persons afflicted with systemic lupuserythematosus is characterized by high levels of expression ofNeutrokine-alpha and/or Neutrokine-alphaSV when compared to thatobserved in individuals not having systemic lupus erythematosus. Thus,Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides and/orpolypeptides of the invention, and/or agonists or antagonists thereof,may be used according to the methods of the invention in the diagnosisand/or prognosis of systemic lupus erythematosus or a subset of systemiclupus erythematosus. For example, a biological sample obtained from aperson suspected of being afflicted with systemic lupus erytheamatosus(“the subject”) may be analyzed for the relative expression level(s) ofNeutrokine-alpha, and/or Neutrokine-alphaSV polynucleotides and/orpolypeptides of the invention. The expression level(s) of one or more ofthese molecules of the invention is (are) then compared to theexpression level(s) of the same molecules of the invention as expressedin a person known not to be afflicted with systemic lupus erythematosus.A significant difference in expression level(s) of Neutrokine-alpha,and/or Neutrokine-alphaSV, polynucleotides and/or polypeptides of theinvention, and/or agonists and/or antagonists thereof, between samplesobtained from the subject and the control suggests that the subject isafflicted with systemic lupus erythematosus or a subset thereof.

Furthermore, there is a direct correlation between the severity ofsystemic lupus erythematosus, or a subset of this disease, and theconcentration of Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides (RNA) and/or polypeptides of the invention. Thus,Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides, (RNA),polypeptides and/or agonists or antagonists of the invention, may beused according to the methods of the invention in prognosis of theseverity of systemic lupus erythematosus or a subset of systemic lupuserythematosus. For example, a biological sample obtained from a personsuspected of being afflicted with systemic lupus erythematosus (“thesubject”) may be analyzed for the relative expression level(s) ofNeutrokine-alpha, and/or Neutrokine-alphaSV polynucleotides and/orpolypeptides of the invention. The expression level(s) of one or more ofthese molecules of the invention is (are) then compared to theexpression level(s) of the same molecules of the invention as expressedin a panel of persons known to represent a range in severities of thisdisease. According to this method, the match of expression level with acharacterized member of the panel indicates the severity of the disease.

In another embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides or Neutrokine-alpha and/orNeutrokine-alphaSV agonists or antagonists (e.g., anti-Neutrokine-alphaand/or anti-Neutrokine-alphaSV antibodies) of the invention are used totreat, diagnose, or prognose an individual having rheumatoid arthritisor a subset of this disease. According to this embodiment, an individualhaving rheumatoid arthritis or a subset of individuals having rheumatoidarthritis expresses aberrantly high levels of Neutrokine-alpha and/orNeutrokine-alpha SV when compared to an individual not having rheumatoidarthritis or this subset of rheumatoid arthritis. Any means describedherein or otherwise known in the art may be applied to detectNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention (e.g., FACS analysis or ELISA detection ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides of the inventionand hybridization or PCR detection of Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides of the invention) and to determinethe expression profile of Neutrokine-alpha and/or Neutrokine-alphaSV,polynucleotides and/or polypeptides of the invention in a biologicalsample.

A biological sample of persons afflicted with rheumatoid arthritis ischaracterized by high levels of expression of Neutrokine-alpha and/orNeutrokine-alphaSV when compared to that observed in individuals nothaving rheumatoid arthritis. Thus, Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides and/or polypeptides of the invention,and/or agonists or antagonists thereof, may be used according to themethods of the invention in the diagnosis and/or prognosis of rheumatoidarthritis or a subset of rheumatoid arthritis. For example, a biologicalsample obtained from a person suspected of being afflicted withrheumatoid arthritis (“the subject”) may be analyzed for the relativeexpression level(s) of Neutrokine-alpha, and/or Neutrokine-alphaSVpolynucleotides and/or polypeptides of the invention. The expressionlevel(s) of one or more of these molecules of the invention is (are)then compared to the expression level(s) of the same molecules of theinvention as expressed in a person known not to be afflicted withrheumatoid arthritis. A significant difference in expression level(s) ofNeutrokine-alpha, and/or Neutrokine-alphaSV, polynucleotides and/orpolypeptides of the invention, and/or agonists and/or antagoniststhereof, between samples obtained from the subject and the controlsuggests that the subject is afflicted with rheumatoid arthritis or asubset thereof.

Thus, the invention provides a diagnostic method useful during diagnosisof a immune system disorder, including cancers of this system, andimmunodeficiencies and/or autoimmune diseases which involves measuringthe expression level of the gene encoding the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide in immune system tissue or other cells orbody fluid from an individual and comparing the measured gene expressionlevel with a standard Neutrokine-alpha and/or Neutrokine-alphaSV geneexpression level, whereby an increase or decrease in the gene expressionlevel compared to the standard is indicative of an immune systemdisorder.

Where a diagnosis of a disorder in the immune system, including, but notlimited to, diagnosis of a tumor, diagnosis of an immunodeficiency,and/or diagnosis of an autoimmune disease, has already been madeaccording to conventional methods, the present invention is useful as aprognostic indicator, whereby patients exhibiting enhanced or depressedNeutrokine-alpha and/or Neutrokine-alphaSV gene expression willexperience a worse clinical outcome relative to patients expressing thegene at a level nearer the standard level.

By analyzing or determining the expression level of the gene encodingthe Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide is intendedqualitatively or quantitatively measuring or estimating the level of theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide or the level ofthe mRNA encoding the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide in a first biological sample either directly (e.g., bydetermining or estimating absolute protein level or mRNA level) orrelatively (e.g., by comparing to the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide level or mRNA level in a secondbiological sample). Preferably, the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide level or mRNA level in the firstbiological sample is measured or estimated and compared to a standardNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide level or mRNAlevel, the standard being taken from a second biological sample obtainedfrom an individual not having the disorder or being determined byaveraging levels from a population of individuals not having a disorderof the immune system. As will be appreciated in the art, once a standardNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide level or mRNAlevel is known, it can be used repeatedly as a standard for comparison.

By “biological sample” is intended any biological sample obtained froman individual, body fluid, cell line, tissue culture, or other sourcewhich contains Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide ormRNA. As indicated, biological samples include body fluids (such assera, plasma, urine, synovial fluid and spinal fluid) which contain freeextracellular domains of the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide, immune system tissue, and other tissue sources found toexpress complete or free extracellular domain of the Neutrokine-alphaand/or Neutrokine-alphaSV or a Neutrokine-alpha and/orNeutrokine-alphaSV receptor. Methods for obtaining tissue biopsies andbody fluids from mammals are well known in the art. Where the biologicalsample is to include mRNA, a tissue biopsy is the preferred source.

The compounds of the present invention are useful for diagnosis,prognosis, or treatment of various immune system-related disorders inmammals, preferably humans. Such disorders include, but are not limitedto tumors (e.g., B cell and monocytic cell leukemias and lymphomas) andtumor metastasis, infections by bacteria, viruses and other parasites,immunodeficiencies, inflammatory diseases, lymphadenopathy, autoimmunediseases (e.g., rheumatoid arthritis, systemic lupus erythematosus,Sjogren's syndrome, mixed connective tissue disease, and inflammatorymyopathies), and graft versus host disease.

Total cellular RNA can be isolated from a biological sample using anysuitable technique such as the single-stepguanidinium-thiocyanate-phenol-chloroform method described inChomczynski and Sacchi, Anal. Biochem. 162:156-159 (1987). Levels ofmRNA encoding the Neutrokine-alpha and/or Neutrokine-alphaSV polypeptideare then assayed using any appropriate method. These include Northernblot analysis, 51 nuclease mapping, the polymerase chain reaction (PCR),reverse transcription in combination with the polymerase chain reaction(RT-PCR), and reverse transcription in combination with the ligase chainreaction (RT-LCR).

Assaying Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide levelsin a biological sample can occur using antibody-based techniques. Forexample, Neutrokine-alpha and/or Neutrokine-alphaSV polypeptideexpression in tissues can be studied with classical immunohistologicalmethods (Jalkanen, M., et al., J. Cell. Biol. 101:976-985 (1985);Jalkanen, M., et al., J. Cell. Biol. 105:3087-3096 (1987)). Otherantibody-based methods useful for detecting Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide gene expression include immunoassays,such as the enzyme linked immunosorbent assay (ELISA) and theradioimmunoassay (RIA). Suitable antibody assay labels are known in theart and include enzyme labels, such as, glucose oxidase, andradioisotopes, such as iodine (¹³¹I, ¹²⁵I, ¹²³I, ¹²¹I) carbon (¹⁴C),sulfur (³⁵S), tritium (³H), indium (^(115m)In, ^(113m)In, ¹¹²In, ¹¹¹In)and technetium (⁹⁹Tc, ^(99m)Tc), thallium (²⁰¹Ti), gallium (⁶⁸Ga, ⁶⁷Ga),palladium (¹⁰³Pd), molybdenum (⁹⁹Mo), xenon (¹³³Xe), fluorine (¹⁸F),¹⁵³Sm, ¹⁷⁷Lu, ¹⁵⁹Gd, ¹⁴⁹Pm, ¹⁴⁰La, ¹⁷⁵Yb, ¹⁶⁶Ho, ⁹⁰Y, ⁴⁷Sc, ¹⁸⁶Re,¹⁸⁸Re, ¹⁴²Pr, ¹⁰⁵Rh, ⁹⁷Ru; luminescent labels, such as luminol; andfluorescent labels, such as fluorescein and rhodamine, and biotin.

Techniques known in the art may be applied to label antibodies of theinvention. Such techniques include, but are not limited to, the use ofbifunctional conjugating agents (see e.g., U.S. Pat. Nos. 5,756,065;5,714,631; 5,696,239; 5,652,361; 5,505,931; 5,489,425; 5,435,990;5,428,139; 5,342,604; 5,274,119; 4,994,560; and 5,808,003; the contentsof each of which are hereby incorporated by reference in its entirety).

The tissue or cell type to be analyzed will generally include thosewhich are known, or suspected, to express the Neutrokine-alpha gene(such as, for example, cells of monocytic lineage) or cells or tissuewhich are known, or suspected, to express the Neutrokine-alpha receptorgene (such as, for example, cells of B cell lineage and the spleen). Theprotein isolation methods employed herein may, for example, be such asthose described in Harlow and Lane (Harlow, E. and Lane, D., 1988,“Antibodies: A Laboratory Manual”, Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y.), which is incorporated herein by reference inits entirety. The isolated cells can be derived from cell culture orfrom a patient. The analysis of cells taken from culture may be anecessary step in the assessment of cells that could be used as part ofa cell-based gene therapy technique or, alternatively, to test theeffect of compounds on the expression of the Neutrokine-alpha gene orNeutrokine-alpha receptor gene.

For example, antibodies, or fragments of antibodies, such as thosedescribed herein, may be used to quantitatively or qualitatively detectthe presence of Neutrokine-alpha gene products or conserved variants orpeptide fragments thereof. This can be accomplished, for example, byimmunofluorescence techniques employing a fluorescently labeled antibodycoupled with light microscopic, flow cytometric, or fluorimetricdetection.

The antibodies (or fragments thereof) or Neutrokine-alpha polypeptidesor polypeptides of the present invention may, additionally, be employedhistologically, as in immunofluorescence, immunoelectron microscopy ornon-immunological assays, for in situ detection of Neutrokine-alpha geneproducts or conserved variants or peptide fragments thereof, or forNeutrokine-alpha binding to Neutrokine-alpha receptor. In situ detectionmay be accomplished by removing a histological specimen from a patient,and applying thereto a labeled antibody or Neutrokine-alpha polypeptideof the present invention. The antibody (or fragment) or Neutrokine-alphapolypeptide is preferably applied by overlaying the labeled antibody (orfragment) onto a biological sample. Through the use of such a procedure,it is possible to determine not only the presence of theNeutrokine-alpha gene product, or conserved variants or peptidefragments, or Neutrokine-alpha polypeptide binding, but also itsdistribution in the examined tissue. Using the present invention, thoseof ordinary skill will readily perceive that any of a wide variety ofhistological methods (such as staining procedures) can be modified inorder to achieve such in situ detection.

Immunoassays and non-immunoassays for Neutrokine-alpha gene products orconserved variants or peptide fragments thereof will typically compriseincubating a sample, such as a biological fluid, a tissue extract,freshly harvested cells, or lysates of cells which have been incubatedin cell culture, in the presence of a detectably labeled antibodycapable of identifying Neutrokine-alpha gene products or conservedvariants or peptide fragments thereof, and detecting the bound antibodyby any of a number of techniques well-known in the art.

Immunoassays and non-immunoassays for Neutrokine-alpha receptor geneproducts or conserved variants or peptide fragments thereof willtypically comprise incubating a sample, such as a biological fluid, atissue extract, freshly harvested cells, or lysates of cells which havebeen incubated in cell culture, in the presence of a detectable orlabeled Neutrokine-alpha polypeptide capable of identifyingNeutrokine-alpha receptor gene products or conserved variants or peptidefragments thereof, and detecting the bound Neutrokine-alpha polypeptideby any of a number of techniques well-known in the art.

The biological sample may be brought in contact with and immobilizedonto a solid phase support or carrier such as nitrocellulose, or othersolid support which is capable of immobilizing cells, cell particles orsoluble proteins. The support may then be washed with suitable buffersfollowed by treatment with the detectably labeled anti-Neutrokine-alphaantibody or detectable Neutrokine-alpha polypeptide. The solid phasesupport may then be washed with the buffer a second time to removeunbound antibody or polypeptide. Optionally the antibody is subsequentlylabeled. The amount of bound label on solid support may then be detectedby conventional means.

By “solid phase support or carrier” is intended any support capable ofbinding an antigen or an antibody. Well-known supports or carriersinclude glass, polystyrene, polypropylene, polyethylene, dextran, nylon,amylases, natural and modified celluloses, polyacrylamides, gabbros, andmagnetite. The nature of the carrier can be either soluble to someextent or insoluble for the purposes of the present invention. Thesupport material may have virtually any possible structuralconfiguration so long as the coupled molecule is capable of binding toan antigen or antibody. Thus, the support configuration may bespherical, as in a bead, or cylindrical, as in the inside surface of atest tube, or the external surface of a rod. Alternatively, the surfacemay be flat such as a sheet, test strip, etc. Preferred supports includepolystyrene beads. Those skilled in the art will know many othersuitable carriers for binding antibody or antigen, or will be able toascertain the same by use of routine experimentation.

The binding activity of a given lot of anti-Neutrokine-alpha antibody orNeutrokine-alpha polypeptide may be determined according to well-knownmethods. Those skilled in the art will be able to determine operativeand optimal assay conditions for each determination by employing routineexperimentation.

In addition to assaying Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide levels or polynucleotide levels in a biological sampleobtained from an individual, Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides or polynucleotides can also be detected in vivo by imaging.For example, in one embodiment of the invention, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide and/or anti-Neutrokine-alpha antibody isused to image B cell lymphomas. In another embodiment, Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides and/or anti-Neutrokine-alphaantibodies and/or Neutrokine-alpha polynucleotides of the invention(e.g., polynucleotides complementary to all or a portion ofNeutrokine-alpha and/or Neutrokine-alphaSV mRNA) is used to imagelymphomas (e.g., monocyte and B cell lymphomas).

Antibody labels or markers for in vivo imaging of Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide include those detectable byX-radiography, NMR, MRI, CAT-scans or ESR. For X-radiography, suitablelabels include radioisotopes such as barium or cesium, which emitdetectable radiation but are not overtly harmful to the subject.Suitable markers for NMR and ESR include those with a detectablecharacteristic spin, such as deuterium, which may be incorporated intothe antibody by labeling of nutrients for the relevant hybridoma. Wherein vivo imaging is used to detect enhanced levels of Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide for diagnosis in humans, it may bepreferable to use human antibodies or “humanized” chimeric monoclonalantibodies. Such antibodies can be produced using techniques describedherein or otherwise known in the art. For example methods for producingchimeric antibodies are known in the art. See, for review, Morrison,Science 229:1202 (1985); Oi et al., BioTechniques 4:214 (1986); Cabillyet al., U.S. Pat. No. 4,816,567; Taniguchi et al., EP 171496; Morrisonet al., EP 173494; Neuberger et al., WO 8601533; Robinson et al., WO8702671; Boulianne et al., Nature 312:643 (1984); Neuberger et al.,Nature 314:268 (1985).

Additionally, any Neutrokine-alpha polypeptide whose presence can bedetected, can be administered. For example, Neutrokine-alphapolypeptides labeled with a radio-opaque or other appropriate compoundcan be administered and visualized in vivo, as discussed, above forlabeled antibodies. Further such Neutrokine-alpha polypeptides can beutilized for in vitro diagnostic procedures.

A Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide-specificantibody or antibody fragment which has been labeled with an appropriatedetectable imaging moiety, such as a radioisotope (for example, ¹³¹I,¹¹²In, ^(99m)Tc, (¹³¹I, ¹²⁵I, ¹²³I, ¹²¹I), carbon (¹⁴C), sulfur (³⁵S),tritium (³H), indium (^(115m)In, ^(113m)In, ¹¹²In, ¹¹¹In), andtechnetium (⁹⁹Tc, ^(99m)Tc), thallium (²⁰¹Ti) gallium (⁶⁸Ga, ⁶⁷Ga),palladium (¹⁰³Pd) molybdenum (⁹⁹Mo), xenon (¹³³Xe), fluorine (¹⁸F),¹⁵³Sm, ¹⁷⁷Lu, ¹⁵⁹Gd, ¹⁴⁹Pm, ¹⁴⁰La, ¹⁷⁵Yb, ¹⁶⁶Ho, ⁹⁰Y, ⁴⁷Sc, ¹⁸⁶Re,¹⁸⁸Re, ¹⁴²Pr, ¹⁰⁵Rh, ⁹⁷Ru), a radio-opaque substance, or a materialdetectable by nuclear magnetic resonance, is introduced (for example,parenterally, subcutaneously or intraperitoneally) into the mammal to beexamined for immune system disorder. It will be understood in the artthat the size of the subject and the imaging system used will determinethe quantity of imaging moiety needed to produce diagnostic images. Inthe case of a radioisotope moiety, for a human subject, the quantity ofradioactivity injected will normally range from about 5 to 20millicuries of ^(99m)Tc. The labeled antibody or antibody fragment willthen preferentially accumulate at the location of cells which containNeutrokine-alpha protein. In vivo tumor imaging is described in S. W.Burchiel et al., “Immunopharmacokinetics of Radiolabeled Antibodies andTheir Fragments” (Chapter 13 in Tumor Imaging: The RadiochemicalDetection of Cancer, S. W. Burchiel and B. A. Rhodes, eds., MassonPublishing Inc. (1982)).

With respect to antibodies, one of the ways in which theanti-Neutrokine-alpha antibody can be detectably labeled is by linkingthe same to an enzyme and using the linked product in an enzymeimmunoassay (EIA) (Voller, A., “The Enzyme Linked Immunosorbent Assay(ELISA)”, 1978, Diagnostic Horizons 2:1-7, Microbiological AssociatesQuarterly Publication, Walkersville, Md.); Voller et al., J. Clin.Pathol. 31:507-520 (1978); Butler, J. E., Meth. Enzymol. 73:482-523(1981); Maggio, E. (ed.), 1980, Enzyme Immunoassay, CRC Press, BocaRaton, Fla.; Ishikawa, E. et al., (eds.), 1981, Enzyme Immunoassay,Kgaku Shoin, Tokyo). The enzyme which is bound to the antibody willreact with an appropriate substrate, preferably a chromogenic substrate,in such a manner as to produce a chemical moiety which can be detected,for example, by spectrophotometric, fluorimetric or by visual means.Enzymes which can be used to detectably label the antibody include, butare not limited to, malate dehydrogenase, staphylococcal nuclease,delta-5-steroid isomerase, yeast alcohol dehydrogenase,alpha-glycerophosphate, dehydrogenase, triose phosphate isomerase,horseradish peroxidase, alkaline phosphatase, asparaginase, glucoseoxidase, beta-galactosidase, ribonuclease, urease, catalase,glucose-6-phosphate dehydrogenase, glucoamylase andacetylcholinesterase. Additionally, the detection can be accomplished bycolorimetric methods which employ a chromogenic substrate for theenzyme. Detection may also be accomplished by visual comparison of theextent of enzymatic reaction of a substrate in comparison with similarlyprepared standards.

Detection may also be accomplished using any of a variety of otherimmunoassays. For example, by radioactively labeling the antibodies orantibody fragments, it is possible to detect Neutrokine-alpha throughthe use of a radioimmunoassay (RIA) (see, for example, Weintraub, B.,Principles of Radioimmunoassays, Seventh Training Course on RadioligandAssay Techniques, The Endocrine Society, March, 1986, which isincorporated by reference herein). The radioactive isotope can bedetected by means including, but not limited to, a gamma counter, ascintillation counter, or autoradiography.

It is also possible to label the antibody with a fluorescent compound.When the fluorescently labeled antibody is exposed to light of theproper wave-length, its presence can then be detected due tofluorescence. Among the most commonly used fluorescent labelingcompounds are fluorescein isothiocyanate, rhodamine, phycoerythrin,phycocyanin, allophycocyanin, ophthaldehyde and fluorescamine.

The antibody can also be detectably labeled using fluorescence emittingmetals such as ¹⁵²Eu, or others of the lanthanide series. These metalscan be attached to the antibody using such metal chelating groups asdiethylenetriaminepentacetic acid (DTPA) or ethylenediaminetetraaceticacid (EDTA).

The antibody also can be detectably labeled by coupling it to achemiluminescent compound. The presence of the chemiluminescent-taggedantibody is then determined by detecting the presence of luminescencethat arises during the course of a chemical reaction. Examples ofparticularly useful chemiluminescent labeling compounds are luminol,isoluminol, theromatic acridinium ester, imidazole, acridinium salt andoxalate ester.

Likewise, a bioluminescent compound may be used to label the antibody ofthe present invention. Bioluminescence is a type of chemiluminescencefound in biological systems in which a catalytic protein increases theefficiency of the chemiluminescent reaction. The presence of abioluminescent protein is determined by detecting the presence ofluminescence. Important bioluminescent compounds for purposes oflabeling include, but are not limited to, luciferin, luciferase andaequorin.

Treatment of Immune System-Related Disorders

As noted above, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides and polypeptides, and anti-Neutrokine-alpha antibodies,are useful for diagnosis of conditions involving abnormally high or lowexpression of Neutrokine-alpha and/or Neutrokine-alphaSV activities.Given the cells and tissues where Neutrokine-alpha and/orNeutrokine-alphaSV is expressed as well as the activities modulated byNeutrokine-alpha and/or Neutrokine-alphaSV, it is readily apparent thata substantially altered (increased or decreased) level of expression ofNeutrokine-alpha and/or Neutrokine-alphaSV in an individual compared tothe standard or “normal” level produces pathological conditions relatedto the bodily system(s) in which Neutrokine-alpha and/orNeutrokine-alphaSV is expressed and/or is active.

It will also be appreciated by one of ordinary skill that, since theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides of the inventionare members of the TNF family, the extracellular domains of therespective proteins may be released in soluble form from the cells whichexpress Neutrokine-alpha and/or Neutrokine-alphaSV by proteolyticcleavage and therefore, when Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide (particularly a soluble form of the respective extracellulardomains) is added from an exogenous source to cells, tissues or the bodyof an individual, the polypeptide will exert its modulating activitieson any of its target cells of that individual. Also, cells expressingthis type II transmembrane protein may be added to cells, tissues or thebody of an individual whereby the added cells will bind to cellsexpressing receptor for Neutrokine-alpha and/or Neutrokine-alphaSVwhereby the cells expressing Neutrokine-alpha and/or Neutrokine-alphaSVcan cause actions (e.g., proliferation or cytotoxicity) on thereceptor-bearing target cells.

In one embodiment, the invention provides a method of deliveringcompositions containing the polypeptides of the invention (e.g.,compositions containing Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides or anti-Neutrokine-alpha and/or anti-Neutrokine-alphaSVantibodies associated with heterologous polypeptides, heterologousnucleic acids, toxins, or prodrugs) to targeted cells, such as, forexample, B cells expressing Neutrokine-alpha and/or Neutrokine-alphaSVreceptor, or monocytes expressing the cell surface bound form ofNeutrokine-alpha and/or Neutrokine-alphaSV. Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or anti-Neutrokine-alpha and/oranti-Neutrokine-alphaSV antibodies of the invention may be associatedwith heterologous polypeptides, heterologous nucleic acids, toxins, orprodrugs via hydrophobic, hydrophilic, ionic and/or covalentinteractions.

In one embodiment, the invention provides a method for the specificdelivery of compositions of the invention to cells by administeringpolypeptides of the invention (e.g., Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or anti-Neutrokine-alpha and/oranti-Neutrokine-alphaSV antibodies) that are associated withheterologous polypeptides or nucleic acids. In one example, theinvention provides a method for delivering a therapeutic protein intothe targeted cell. In another example, the invention provides a methodfor delivering a single stranded nucleic acid (e.g., antisense orribozymes) or double stranded nucleic acid (e.g., DNA that can integrateinto the cell's genome or replicate episomally and that can betranscribed) into the targeted cell.

In another embodiment, the invention provides a method for the specificdestruction of cells (e.g., the destruction of tumor cells) byadministering polypeptides of the invention (e.g., Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides or anti-Neutrokine-alpha and/oranti-Neutrokine-alphaSV antibodies) in association with toxins orcytotoxic prodrugs.

In a specific embodiment, the invention provides a method for thespecific destruction of cells of B cell lineage (e.g., B cell relatedleukemias or lymphomas) by administering Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides in association with toxins or cytotoxicprodrugs.

In another specific embodiment, the invention provides a method for thespecific destruction of cells of monocytic lineage (e.g., monocyticleukemias or lymphomas) by administering anti-Neutrokine-alpha and/oranti-Neutrokine-alphaSV antibodies in association with toxins orcytotoxic prodrugs.

By “toxin” is meant compounds that bind and activate endogenouscytotoxic effector systems, radioisotopes, holotoxins, modified toxins,catalytic subunits of toxins, cytotoxins (cytotoxic agents), or anymolecules or enzymes not normally present in or on the surface of a cellthat under defined conditions cause the cell's death. Toxins that may beused according to the methods of the invention include, but are notlimited to, radioisotopes known in the art, compounds such as, forexample, antibodies (or complement fixing containing portions thereof)that bind an inherent or induced endogenous cytotoxic effector system,thymidine kinase, endonuclease, RNAse, alpha toxin, ricin, abrin,Pseudomonas exotoxin A, diphtheria toxin, saporin, momordin, gelonin,pokeweed antiviral protein, alpha-sarcin and cholera toxin. “Toxin” alsoincludes a cytostatic or cytocidal agent, a therapeutic agent or aradioactive metal ion, e.g., alpha-emitters such as, for example, ²¹³Bi,or other radioisotopes such as, for example, ¹⁰³Pd, ¹³³Xe, ¹³¹I, ⁶⁸Ge,⁵⁷Co, ⁶⁵Zn, ⁸⁵Sr, ³²P, ³⁵S, ⁹⁰Y, ¹⁵³Sm, ¹⁵³Gd, ¹⁶⁹Yb, ⁵¹Cr, ⁵⁴Mn, ⁷⁵Se,¹¹³Sn, ⁹⁰Yttrium, ¹¹⁷Tin, ¹⁸⁶Rhenium, ¹⁶⁶Holmium, and ¹⁸⁸Rhenium;luminescent labels, such as luminol; and fluorescent labels, such asfluorescein and rhodamine, and biotin.

Techniques known in the art may be applied to label antibodies of theinvention. Such techniques include, but are not limited to, the use ofbifunctional conjugating agents (see e.g., U.S. Pat. Nos. 5,756,065;5,714,631; 5,696,239; 5,652,361; 5,505,931; 5,489,425; 5,435,990;5,428,139; 5,342,604; 5,274,119; 4,994,560; and 5,808,003; the contentsof each of which are hereby incorporated by reference in its entirety).A cytotoxin or cytotoxic agent includes any agent that is detrimental tocells. Examples include paclitaxol, cytochalasin B, gramicidin D,ethidium bromide, emetine, mitomycin, etoposide, tenoposide,vincristine, vinblastine, colchicin, doxorubicin, daunorubicin,dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D,1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine,propranolol, and puromycin and analogs or homologs thereof. Therapeuticagents include, but are not limited to, antimetabolites (e.g.,methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine,5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine,thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU),cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycinC, and cis-dichlorodiamine platinum (II) (DDP) cisplatin),anthracyclines (e.g., daunorubicin (formerly daunomycin) anddoxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin),bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents(e.g., vincristine and vinblastine).

By “cytotoxic prodrug” is meant a non-toxic compound that is convertedby an enzyme, normally present in the cell, into a cytotoxic compound.Cytotoxic prodrugs that may be used according to the methods of theinvention include, but are not limited to, glutamyl derivatives ofbenzoic acid mustard alkylating agent, phosphate derivatives ofetoposide or mitomycin C, cytosine arabinoside, daunorubisin, andphenoxyacetamide derivatives of doxorubicin.

It will be appreciated that conditions caused by a decrease in thestandard or normal level of Neutrokine-alpha and/or Neutrokine-alphaSVactivity in an individual, particularly disorders of the immune system,can be treated by administration of Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide (in the form of soluble extracellulardomain or cells expressing the complete protein) or agonist. Thus, theinvention also provides a method of treatment of an individual in needof an increased level of Neutrokine-alpha and/or Neutrokine-alphaSVactivity comprising administering to such an individual a pharmaceuticalcomposition comprising an amount of an isolated Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide of the invention, or agonist thereof,effective to increase the Neutrokine-alpha and/or Neutrokine-alphaSVactivity level in such an individual.

It will also be appreciated that conditions caused by a increase in thestandard or normal level of Neutrokine-alpha and/or Neutrokine-alphaSVactivity in an individual, particularly disorders of the immune system,can be treated by administration of Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides (in the form of soluble extracellulardomain or cells expressing the complete protein) or antagonist (e.g., ananti-Neutrokine-alpha antibody). Thus, the invention also provides amethod of treatment of an individual in need of an decreased level ofNeutrokine-alpha and/or Neutrokine-alphaSV activity comprisingadministering to such an individual a pharmaceutical compositioncomprising an amount of an isolated Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide of the invention, or antagonist thereof,effective to decrease the Neutrokine-alpha and/or Neutrokine-alphaSVactivity level in such an individual.

Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention, or agonists of Neutrokine-alpha and/orNeutrokine-alphaSV, can be used in the treatment of infectious agents.For example, by increasing the immune response, particularly increasingthe proliferation and differentiation of B cells, infectious diseasesmay be treated. The immune response may be increased by either enhancingan existing immune response, or by initiating a new immune response.Alternatively, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides, or agonists of Neutrokine-alpha and/orNeutrokine-alphaSV, may also directly inhibit the infectious agent,without necessarily eliciting an immune response.

Viruses are one example of an infectious agent that can cause disease orsymptoms that can be treated by Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides, or agonists ofNeutrokine-alpha and/or Neutrokine-alphaSV. Examples of viruses,include, but are not limited to the following DNA and RNA viruses andviral families: Arbovirus, Adenoviridae, Arenaviridae, Arterivirus,Birnaviridae, Bunyaviridae, Caliciviridae, Circoviridae, Coronaviridae,Dengue, EBV, HIV, Flaviviridae, Hepadnaviridae (Hepatitis),Herpesviridae (such as, Cytomegalovirus, Herpes Simplex, Herpes Zoster),Mononegavirus (e.g., Paramyxoviridae, Morbillivirus, Rhabdoviridae),Orthomyxoviridae (e.g., Influenza A, Influenza B, and parainfluenza),Papiloma virus, Papovaviridae, Parvoviridae, Picornaviridae, Poxyiridae(such as Smallpox or Vaccinia), Reoviridae (e.g., Rotavirus),Retroviridae (HTLV-I, HTLV-II, Lentivirus), and Togaviridae (e.g.,Rubivirus). Viruses falling within these families can cause a variety ofdiseases or symptoms, including, but not limited to: arthritis,bronchiollitis, respiratory syncytial virus, encephalitis, eyeinfections (e.g., conjunctivitis, keratitis), chronic fatigue syndrome,hepatitis (A, B, C, E, Chronic Active, Delta), Japanese B encephalitis,Junin, Chikungunya, Rift Valley fever, yellow fever, meningitis,opportunistic infections (e.g., AIDS), pneumonia, Burkitt's Lymphoma,chickenpox, hemorrhagic fever, Measles, Mumps, Parainfluenza, Rabies,the common cold, Polio, leukemia, Rubella, sexually transmitteddiseases, skin diseases (e.g., Kaposi's, warts), and viremia.Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides, or agonists or antagonists of Neutrokine-alpha and/orNeutrokine-alphaSV, can be used to treat, prevent, diagnose, and/ordetect any of these symptoms or diseases. In specific embodiments,Neutrokine alpha polynucleotides, polypeptides, or agonists are used totreat, prevent, and/or diagnose: meningitis, Dengue, EBV, and/orhepatitis (e.g., hepatitis B). In an additional specific embodimentNeutrokine alpha polynucleotides, polypeptides, or agonists are used totreat patients nonresponsive to one or more other commercially availablehepatitis vaccines. In a further specific embodiment, Neutrokine alphapolynucleotides, polypeptides, or agonists are used to treat, prevent,and/or diagnose AIDS. In an additional specific embodimentNeutrokine-alpha and/or Neutrokine-alphaSV and/or Neutrokine-alphaReceptor polynucleotides, polypeptides, agonists, and/or antagonists areused to treat, prevent, and/or diagnose patients with cryptosporidiosis.

Similarly, bacterial or fungal agents that can cause disease or symptomsand that can be treated by Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides, or agonists or antagonists ofNeutrokine-alpha and/or Neutrokine-alphaSV, include, but are not limitedto, the following Gram-Negative and Gram-positive bacteria and bacterialfamilies and fungi: Actinomycetales (e.g., Corynebacterium,Mycobacterium, Norcardia), Cryptococcus neoformans, Aspergillosis,Bacillaceae (e.g., Anthrax, Clostridium), Bacteroidaceae, Blastomycosis,Bordetella, Borrelia (e.g., Borrelia burgdorferi, Brucellosis,Candidiasis, Campylobacter, Coccidioidomycosis, Cryptococcosis,Dermatocycoses, E. coli (e.g., Enterotoxigenic E. coli andEnterohemorrhagic E. coli), Enterobacteriaceae (Klebsiella, Salmonella(e.g., Salmonella typhi, and Salmonella paratyphi), Serratia, Yersinia),Erysipelothrix, Helicobacter, Legionellosis, Leptospirosis, Listeria(e.g, Listeria monocytogenes), Mycoplasmatales, Mycobacterium leprae,Vibrio cholerae, Neisseriaceae (e.g., Acinetobacter, Gonorrhea,Menigococcal), Neisseria meningitidis, Pasteurellacea Infections (e.g.,Actinobacillus, Heamophilus (e.g., Heamophilus influenza type B),Pasteurella), Pseudomonas, Rickettsiaceae, Chlamydiaceae, Syphilis,Shigella spp., Staphylococcal, Meningiococcal, Pneumococcal andStreptococcal (e.g., Streptococcus pneumoniae and Group BStreptococcus). These bacterial or fungal families can cause thefollowing diseases or symptoms, including, but not limited to:bacteremia, endocarditis, eye infections (conjunctivitis, tuberculosis,uveitis), gingivitis, opportunistic infections (e.g., AIDS relatedinfections), paronychia, prosthesis-related infections, Reiter'sDisease, respiratory tract infections, such as Whooping Cough orEmpyema, sepsis, Lyme Disease, Cat-Scratch Disease, Dysentery,Paratyphoid Fever, food poisoning, Typhoid, pneumonia, Gonorrhea,meningitis (e.g., meningitis types A and B), Chlamydia, Syphilis,Diphtheria, Leprosy, Paratuberculosis, Tuberculosis, Lupus, Botulism,gangrene, tetanus, impetigo, Rheumatic Fever, Scarlet Fever, sexuallytransmitted diseases, skin diseases (e.g., cellulitis, dermatocycoses),toxemia, urinary tract infections, wound infections. Neutrokine-alphaand/or Neutrokine-alphaSV polynucleotides or polypeptides, or agonistsor antagonists of Neutrokine-alpha and/or Neutrokine-alphaSV, can beused to treat, prevent, diagnose, and/or detect any of these symptoms ordiseases. In specific embodiments, Neutrokine alpha polynucleotides,polypeptides, or agonists thereof are used to treat, prevent, and/ordiagnose: tetanus, Diptheria, botulism, and/or meningitis type B.

Moreover, parasitic agents causing disease or symptoms that can betreated by Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides, or agonists of Neutrokine-alpha and/or Neutrokine-alphaSV,include, but not limited to, the following families or class: Amebiasis,Babesiosis, Coccidiosis, Cryptosporidiosis, Dientamoebiasis, Dourine,Ectoparasitic, Giardiasis, Helminthiasis, Leishmaniasis, Theileriasis,Toxoplasmosis, Trypanosomiasis, and Trichomonas and Sporozoans (e.g.,Plasmodium virax, Plasmodium falciparum, Plasmodium malariae andPlasmodium ovale). These parasites can cause a variety of diseases orsymptoms, including, but not limited to: Scabies, Trombiculiasis, eyeinfections, intestinal disease (e.g., dysentery, giardiasis), liverdisease, lung disease, opportunistic infections (e.g., AIDS related),malaria, pregnancy complications, and toxoplasmosis. Neutrokine-alphaand/or Neutrokine-alphaSV polynucleotides or polypeptides, or agonistsor antagonists of Neutrokine-alpha and/or Neutrokine-alphaSV, can beused to treat, prevent, diagnose, and/or detect any of these symptoms ordiseases. In specific embodiments, Neutrokine alpha polynucleotides,polypeptides, or agonists thereof are used to treat, prevent, and/ordiagnose malaria.

In another embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides of the invention and/or agonists and/orantagonists thereof, are used to treat, prevent, and/or diagnose innerear infection (such as, for example, otitis media), as well as otherinfections characterized by infection with Streptococcus pneumoniae andother pathogenic organisms.

In a specific embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides, or agonists or antagonists thereof(e.g., anti-Neutrokine-alpha, and/or anti-Neutrokine-alphaSV antibodies)are used to treat or prevent a disorder characterized by deficient serumimmunoglobulin production, recurrent infections, and/or immune systemdysfunction. Moreover, Neutrokine-alpha, and/or Neutrokine-alphaSVpolynucleotides or polypeptides, or agonists or antagonists thereof(e.g., anti-Neutrokine-alpha, and/or anti-Neutrokine-alphaSV antibodies)may be used to treat or prevent infections of the joints, bones, skin,and/or parotid glands, blood-borne infections (e.g., sepsis, meningitis,septic arthritis, and/or osteomyelitis), autoimmune diseases (e.g.,those disclosed herein), inflammatory disorders, and malignancies,and/or any disease or disorder or condition associated with theseinfections, diseases, disorders and/or malignancies) including, but notlimited to, CVID, other primary immune deficiencies, HIV disease, CLL,recurrent bronchitis, sinusitis, otitis media, conjunctivitis,pneumonia, hepatitis, meningitis, herpes zoster (e.g., severe herpeszoster), and/or pheumocystis carnii.

Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention, or agonists or antagonists thereof, maybe used to diagnose, prognose, treat or prevent one or more of thefollowing diseases or disorders, or conditions associated therewith:primary immunodeficiencies, immune-mediated thrombocytopenia, Kawasakisyndrome, bone marrow transplant (e.g., recent bone marrow transplant inadults or children), chronic B-cell lymphocytic leukemia, HIV infection(e.g., adult or pediatric HIV infection), chronic inflammatorydemyelinating polyneuropathy, and post-transfusion purpura.

Additionally, Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotidesor polypeptides of the invention, or agonists or antagonists thereof,may be used to diagnose, prognose, treat or prevent one or more of thefollowing diseases, disorders, or conditions associated therewith,Guillain-Barre syndrome, anemia (e.g., anemia associated with parvovirusB19, patients with stable multiple myeloma who are at high risk forinfection (e.g., recurrent infection), autoimmune hemolytic anemia(e.g., warm-type autoimmune hemolytic anemia), thrombocytopenia (e.g.,neonatal thrombocytopenia), and immune-mediated neutropenia),transplantation (e.g., cytamegalovirus (CMV)-negative recipients ofCMV-positive organs), hypogammaglobulinemia (e.g., hypogammaglobulinemicneonates with risk factor for infection or morbidity), epilepsy (e.g.,intractable epilepsy), systemic vasculitic syndromes, myasthenia gravis(e.g., decompensation in myasthenia gravis), dermatomyositis, andpolymyositis.

Additional preferred embodiments of the invention include, but are notlimited to, the use of Neutrokine-alpha and/or Neutrokine-alpha SVpolypeptides, Neutrokine-alpha and/or Neutrokine-alpha SVpolynucleotides, and functional agonists thereof, in the followingapplications:

Administration to an animal (e.g., mouse, rat, rabbit, hamster, guineapig, pigs, micro-pig, chicken, camel, goat, horse, cow, sheep, dog, cat,non-human primate, and human, most preferably human) to boost the immunesystem to produce increased quantities of one or more antibodies (e.g.,IgG, IgA, IgM, and IgE), to induce higher affinity antibody production(e.g., IgG, IgA, IgM, and IgE), and/or to increase an immune response.In a specific nonexclusive embodiment, Neutrokine-alpha polypeptides ofthe invention, and/or agonists thereof, are administered to boost theimmune system to produce increased quantities of IgG. In anotherspecific nonexclusive embodiment, Neutrokine-alpha polypeptides of theinvention and/or agonists thereof, are administered to boost the immunesystem to produce increased quantities of IgA. In another specificnonexclusive embodiment, Neutrokine-alpha polypeptides of the inventionand/or agonists thereof, are administered to boost the immune system toproduce increased quantities of IgM.

Administration to an animal (including, but not limited to, those listedabove, and also including transgenic animals) incapable of producingfunctional endogenous antibody molecules or having an otherwisecompromised endogenous immune system, but which is capable of producinghuman immunoglobulin molecules by means of a reconstituted or partiallyreconstituted immune system from another animal (see, e.g., publishedPCT Application Nos. WO98/24893, WO/9634096, WO/9633735, andWO/9110741).

A vaccine adjuvant that enhances immune responsiveness to specificantigen. In a specific embodiment, the vaccine adjuvant is aNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide described herein.In another specific embodiment, the vaccine adjuvant is aNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotide describedherein (i.e., the Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotide is a genetic vaccine adjuvant). As discussed herein,Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides may beadministered using techniques known in the art, including but notlimited to, liposomal delivery, recombinant vector delivery, injectionof naked DNA, and gene gun delivery.

An adjuvant to enhance tumor-specific immune responses.

An adjuvant to enhance anti-viral immune responses. Anti-viral immuneresponses that may be enhanced using the compositions of the inventionas an adjuvant, include, but are not limited to, virus and virusassociated diseases or symptoms described herein or otherwise known inthe art. In specific embodiments, the compositions of the invention areused as an adjuvant to enhance an immune response to a virus, disease,or symptom selected from the group consisting of: AIDS, meningitis,Dengue, EBV, and hepatitis (e.g., hepatitis B). In another specificembodiment, the compositions of the invention are used as an adjuvant toenhance an immune response to a virus, disease, or symptom selected fromthe group consisting of: HIV/AIDS, Respiratory syncytial virus, Dengue,Rotavirus, Japanese B encephalitis, Influenza A and B, Parainfluenza,Measles, Cytomegalovirus, Rabies, Junin, Chikungunya, Rift Valley fever,Herpes simplex, and yellow fever. In another specific embodiment, thecompositions of the invention are used as an adjuvant to enhance animmune response to the HIV gp120 antigen.

An adjuvant to enhance anti-bacterial or anti-fungal immune responses.Anti-bacterial or anti-fungal immune responses that may be enhancedusing the compositions of the invention as an adjuvant, include bacteriaor fungus and bacteria or fungus associated diseases or symptomsdescribed herein or otherwise known in the art. In specific embodiments,the compositions of the invention are used as an adjuvant to enhance animmune response to a bacteria or fungus, disease, or symptom selectedfrom the group consisting of: tetanus, Diphtheria, botulism, andmeningitis type B. In another specific embodiment, the compositions ofthe invention are used as an adjuvant to enhance an immune response to abacteria or fungus, disease, or symptom selected from the groupconsisting of: Vibrio cholerae, Mycobacterium leprae, Salmonella typhi,Salmonella paratyphi, Neisseria meningitidis, Streptococcus pneumoniae,Group B streptococcus, Shigella spp., Enterotoxigenic Escherichia coli,Enterohemorrhagic E. coli, Borrelia burgdorferi, and Plasmodium(malaria).

An adjuvant to enhance anti-parasitic immune responses. Anti-parasiticimmune responses that may be enhanced using the compositions of theinvention as an adjuvant, include parasite and parasite associateddiseases or symptoms described herein or otherwise known in the art. Inspecific embodiments, the compositions of the invention are used as anadjuvant to enhance an immune response to a parasite. In anotherspecific embodiment, the compositions of the invention are used as anadjuvant to enhance an immune response to Plasmodium (malaria).

As a stimulator of B cell responsiveness to pathogens.

As an agent that elevates the immune status of an individual prior totheir receipt of immunosuppressive therapies.

As an agent to induce higher affinity antibodies.

As an agent to increase serum immunoglobulin concentrations.

As an agent to accelerate recovery of immunocompromised individuals.

As an agent to boost immunoresponsiveness among aged populations.

As an immune system enhancer prior to, during, or after bone marrowtransplant and/or other transplants (e.g., allogeneic or xenogeneicorgan transplantation). With respect to transplantation, compositions ofthe invention may be administered prior to, concomitant with, and/orafter transplantation. In a specific embodiment, compositions of theinvention are administered after transplantation, prior to the beginningof recovery of T-cell populations. In another specific embodiment,compositions of the invention are first administered aftertransplantation after the beginning of recovery of T cell populations,but prior to full recovery of B cell populations.

As an agent to boost immunoresponsiveness among B cell immunodeficientindividuals, such as, for example, an individual who has undergone apartial or complete splenectomy. B cell immunodeficiencies that may beameliorated or treated by administering the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, include, but are not limited to, severe combinedimmunodeficiency (SCID)-X linked, SCID-autosomal, adenosine deaminasedeficiency (ADA deficiency), X-linked agammaglobulinemia (XLA), Bruton'sdisease, congenital agammaglobulinemia, X-linked infantileagammaglobulinemia, acquired agammaglobulinemia, adult onsetagammaglobulinemia, late-onset agammaglobulinemia, dysgammaglobulinemia,hypogammaglobulinemia, transient hypogammaglobulinemia of infancy,unspecified hypogammaglobulinemia, agammaglobulinemia, common variableimmunodeficiency (CVID) (acquired), Wiskott-Aldrich Syndrome (WAS),X-linked immunodeficiency with hyper IgM, non X-linked immunodeficiencywith hyper IgM, selective IgA deficiency, IgG subclass deficiency (withor without IgA deficiency), antibody deficiency with normal or elevatedIgs, immunodeficiency with thymoma, Ig heavy chain deletions, kappachain deficiency, B cell lymphoproliferative disorder (BLPD), selectiveIgM immunodeficiency, recessive agammaglobulinemia (Swiss type),reticular dysgenesis, neonatal neutropenia, severe congenitalleukopenia, thymic alymphoplasia-aplasia or dysplasia withimmunodeficiency, ataxia-telangiectasia, short limbed dwarfism, X-linkedlymphoproliferative syndrome (XLP), Nezelof syndrome-combinedimmunodeficiency with Igs, purine nucleoside phosphorylase deficiency(PNP), MHC Class II deficiency (Bare Lymphocyte Syndrome) and severecombined immunodeficiency.

As an agent to boost immunoresponsiveness among individuals having anacquired loss of B cell function. Conditions resulting in an acquiredloss of B cell function that may be ameliorated or treated byadministering the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides or polynucleotides of the invention, or agonists thereof,include, but are not limited to, HIV Infection, AIDS, bone marrowtransplant, and B cell chronic lymphocytic leukemia (CLL).

As an agent to boost immunoresponsiveness among individuals having atemporary immune deficiency. Conditions resulting in a temporary immunedeficiency that may be ameliorated or treated by administering theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides orpolynucleotides of the invention, or agonists thereof, include, but arenot limited to, recovery from viral infections (e.g., influenza),conditions associated with malnutrition, recovery from infectiousmononucleosis, or conditions associated with stress, recovery frommeasles, recovery from blood transfusion, recovery from surgery.

As a regulator of antigen presentation by monocytes, dendritic cells,and/or B-cells. In one embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides (in soluble, membrane-bound ortransmembrane forms) or polynucleotides enhance antigen presentation orantagonize antigen presentation in vitro or in vivo. Moreover, inrelated embodiments, this enhancement or antagonization of antigenpresentation may be useful in anti-tumor treatment or to modulate theimmune system.

As a mediator of mucosal immune responses. The expression ofNeutrokine-alpha by monocytes and the responsiveness of B cells to thisfactor suggests that it may be involved in exchange of signals between Bcells and monocytes or their differentiated progeny. This activity is inmany ways analogous to the CD40-CD154 signaling between B cells and Tcells. Neutrokine-alpha may therefore be an important regulator of Tcell independent immune responses to environmental pathogens. Inparticular, the unconventional B cell populations (CD5+) that areassociated with mucosal sites and responsible for much of the innateimmunity in humans may respond to Neutrokine-alpha thereby enhancing anindividual's protective immune status.

As an agent to direct an individual's immune system towards developmentof a humoral response (i.e. TH2) as opposed to a TH1 cellular response.

As a means to induce tumor proliferation and thus make it moresusceptible to anti-neoplastic agents. For example, multiple myeloma isa slowly dividing disease and is thus refractory to virtually allanti-neoplastic regimens. If these cells were forced to proliferate morerapidly their susceptibility profile would likely change.

As a B cell specific binding protein to which specific activators orinhibitors of cell growth may be attached. The result would be to focusthe activity of such activators or inhibitors onto normal, diseased, orneoplastic B cell populations.

As a means of detecting B-lineage cells by virtue of its specificity.This application may require labeling the protein with biotin or otheragents (e.g., as described herein) to afford a means of detection.

As a stimulator of B cell production in pathologies such as AIDS,chronic lymphocyte disorder and/or Common Variable Immunodeficiency.

As part of a B cell selection device the function of which is to isolateB cells from a heterogenous mixture of cell types. Neutrokine-alphacould be coupled to a solid support to which B cells would thenspecifically bind. Unbound cells would be washed out and the bound cellssubsequently eluted. A nonlimiting use of this selection would be toallow purging of tumor cells from, for example, bone marrow orperipheral blood prior to transplant.

As a therapy for generation and/or regeneration of lymphoid tissuesfollowing surgery, trauma or genetic defect.

As a gene-based therapy for genetically inherited disorders resulting inimmuno-incompetence such as observed among SCID patients.

As an antigen for the generation of antibodies to inhibit or enhanceNeutrokine-alpha mediated responses.

As a means of activating monocytes/macrophages to defend againstparasitic diseases that effect monocytes such as Leshmania.

As pretreatment of bone marrow samples prior to transplant. Suchtreatment would increase B cell representation and thus acceleraterecovery.

As a means of regulating secreted cytokines that are elicited byNeutrokine-alpha.

Neutrokine-alpha or Neutrokine-alphaSV polypeptides or polynucleotidesof the invention, or agonists may be used to modulate IgE concentrationsin vitro or in vivo.

Additionally, Neutrokine-alpha and/or Neutrokine-alphaSV polypeptides orpolynucleotides of the invention, or agonists thereof, may be used totreat, prevent, and/or diagnose IgE-mediated allergic reactions. Suchallergic reactions include, but are not limited to, asthma, rhinitis,and eczema.

In a specific embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides or polynucleotides of the invention, or agonists thereof,are administered to treat, prevent, diagnose, and/or ameliorateselective IgA deficiency.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate ataxia-telangiectasia.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate common variable immunodeficiency.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate X-linked agammaglobulinemia.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate severe combined immunodeficiency (SCID).

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate Wiskott-Aldrich syndrome.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate X-linked Ig deficiency with hyper IgM.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists or antagonists (e.g., anti-Neutrokine-alpha antibodies)thereof, are administered to treat, prevent, and/or diagnose chronicmyelogenous leukemia, acute myelogenous leukemia, leukemia, hystiocyticleukemia, monocytic leukemia (e.g., acute monocytic leukemia), leukemicreticulosis, Shilling Type monocytic leukemia, and/or other leukemiasderived from monocytes and/or monocytic cells and/or tissues.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate monocytic leukemoid reaction, as seen, for example, withtuberculosis.

In another specific embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, oragonists thereof, are administered to treat, prevent, diagnose, and/orameliorate monocytic leukocytosis, monocytic leukopenia, monocytopenia,and/or monocytosis.

In a specific embodiment, Neutrokine-alpha, and Neutrokine-alphaSVpolynucleotides or polypeptides of the invention, and/oranti-Neutrokine-alpha antibodies and/or agonists or antagonists thereof,are used to treat, prevent, detect, and/or diagnose primary B lymphocytedisorders and/or diseases, and/or conditions associated therewith. Inone embodiment, such primary B lymphocyte disorders, diseases, and/orconditions are characterized by a complete or partial loss of humoralimmunity. Primary B lymphocyte disorders, diseases, and/or conditionsassociated therewith that are characterized by a complete or partialloss of humoral immunity and that may be prevented, treated, detectedand/or diagnosed with compositions of the invention include, but are notlimited to, X-Linked Agammaglobulinemia (XLA), severe combinedimmunodeficiency disease (SCID), and selective IgA deficiency.

In a preferred embodiment, Neutrokine-alpha and Neutrokine-alphaSVpolynucleotides, polypeptides, and/or agonists and/or antagoniststhereof are used to treat, prevent, and/or diagnose diseases ordisorders affecting or conditions associated with any one or more of thevarious mucous membranes of the body. Such diseases or disordersinclude, but are not limited to, for example, mucositis, mucoclasis,mucocolitis, mucocutaneous leishmaniasis (such as, for example, Americanleishmaniasis, leishmaniasis americana, nasopharyngeal leishmaniasis,and New World leishmaniasis), mucocutaneous lymph node syndrome (forexample, Kawasaki disease), mucoenteritis, mucoepidermoid carcinoma,mucoepidermoid tumor, mucoepithelial dysplasia, mucoid adenocarcinoma,mucoid degeneration, myxoid degeneration; myxomatous degeneration;myxomatosis, mucoid medial degeneration (for example, cystic medialnecrosis), mucolipidosis (including, for example, mucolipidosis I,mucolipidosis II, mucolipidosis III, and mucolipidosis IV), mucolysisdisorders, mucomembranous enteritis, mucoenteritis,mucopolysaccharidosis (such as, for example, type Imucopolysaccharidosis (i.e., Hurler's syndrome), type ISmucopolysaccharidosis (i.e., Scheie's syndrome or type Vmucopolysaccharidosis), type II mucopolysaccharidosis (i.e., Hunter'ssyndrome), type III mucopolysaccharidosis (i.e., Sanfilippo's syndrome),type IV mucopolysaccharidosis (i.e., Morquio's syndrome), type VImucopolysaccharidosis (i.e., Maroteaux-Lamy syndrome), type VIImucopolysaccharidosis (i.e., mucopolysaccharidosis due tobeta-glucuronidase deficiency), and mucosulfatidosis),mucopolysacchariduria, mucopurulent conjunctivitis, mucopus,mucormycosis (i.e., zygomycosis), mucosal disease (i.e., bovine virusdiarrhea), mucous colitis (such as, for example, mucocolitis andmyxomembranous colitis), and mucoviscidosis (such as, for example,cystic fibrosis, cystic fibrosis of the pancreas, Clarke-Hadfieldsyndrome, fibrocystic disease of the pancreas, mucoviscidosis, andviscidosis). In a highly preferred embodiment, Neutrokine-alpha, and/orNeutrokine-alphaSV polynucleotides, polypeptides, and/or agonists and/orantagonists thereof are used to treat, prevent, and/or diagnosemucositis, especially as associated with chemotherapy.

In a preferred embodiment, Neutrokine-alpha, and/or Neutrokine-alphaSVpolynucleotides, polypeptides, and/or agonists and/or antagoniststhereof are used to treat, prevent, and/or diagnose diseases ordisorders affecting or conditions associated with sinusitis.

An additional condition, disease or symptom that can be treated,prevented, and/or diagnosed by Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides, or agonists ofNeutrokine-alpha and/or Neutrokine-alphaSV, is osteomyelitis.

An additional condition, disease or symptom that can be treated,prevented, and/or diagnosed by Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides, or agonists ofNeutrokine-alpha and/or Neutrokine-alphaSV, is endocarditis.

All of the above described applications as they may apply to veterinarymedicine.

Antagonists of Neutrokine-alpha include binding and/or inhibitoryantibodies, antisense nucleic acids, ribozymes, and Neutrokine-alphapolypeptides of the invention. These would be expected to reverse manyof the activities of the ligand described above as well as find clinicalor practical application as:

A means of blocking various aspects of immune responses to foreignagents or self. Examples include autoimmune disorders such as lupus, andarthritis, as well as immunoresponsiveness to skin allergies,inflammation, bowel disease, injury and pathogens. Although our currentdata speaks directly to the potential role of Neutrokine-alpha in B celland monocyte related pathologies, it remains possible that other celltypes may gain expression or responsiveness to Neutrokine-alpha. Thus,Neutrokine-alpha may, like CD40 and its ligand, be regulated by thestatus of the immune system and the microenvironment in which the cellis located.

A therapy for preventing the B cell proliferation and Ig secretionassociated with autoimmune diseases such as idiopathic thrombocytopenicpurpura, systemic lupus erythematosus and MS.

An inhibitor of graft versus host disease or transplant rejection.

A therapy for B cell malignancies such as ALL, Hodgkins disease,non-Hodgkins lymphoma, Chronic lymphocyte leukemia, plasmacytomas,multiple myeloma, Burkitt's lymphoma, and EBV-transformed diseases.

A therapy for chronic hypergammaglobulinemeia evident in such diseasesas monoclonalgammopathy of undetermined significance (MGUS),Waldenstrom's disease, related idiopathic monoclonalgammopathies, andplasmacytomas.

A therapy for decreasing cellular proliferation of Large B-cellLymphomas.

A means of decreasing the involvement of B cells and Ig associated withChronic Myelogenous Leukemia.

An immunosuppressive agent(s).

Neutrokine-alpha or Neutrokine-alphaSV polypeptides or polynucleotidesof the invention, or antagonists may be used to modulate IgEconcentrations in vitro or in vivo.

In another embodiment, administration of Neutrokine-alpha orNeutrokine-alphaSV polypeptides or polynucleotides of the invention, orantagonists thereof, may be used to treat, prevent, and/or diagnoseIgE-mediated allergic reactions including, but not limited to, asthma,rhinitis, and eczema.

An inhibitor of signaling pathways involving ERK1, COX2 and Cyclin D2which have been associated with Neutrokine-alpha induced B cellactivation.

The above-recited applications have uses in a wide variety of hosts.Such hosts include, but are not limited to, human, murine, rabbit, goat,guinea pig, camel, horse, mouse, rat, hamster, pig, micro-pig, chicken,goat, cow, sheep, dog, cat, non-human primate, and human. In specificembodiments, the host is a mouse, rabbit, goat, guinea pig, chicken,rat, hamster, pig, sheep, dog or cat. In preferred embodiments, the hostis a mammal. In most preferred embodiments, the host is a human.

The agonists and antagonists may be employed in a composition with apharmaceutically acceptable carrier, e.g., as described herein.

The antagonists may be employed for instance to inhibitNeutrokine-alpha-mediated and/or Neutrokine-alphaSV-mediated chemotaxisand activation of macrophages and their precursors, and of neutrophils,basophils, B lymphocytes and some T-cell subsets, e.g., activated andCD8 cytotoxic T cells and natural killer cells, in certain auto-immuneand chronic inflammatory and infective diseases. Examples of auto-immunediseases include multiple sclerosis, and insulin-dependent diabetes. Theantagonists may also be employed to treat, prevent, and/or diagnoseinfectious diseases including silicosis, sarcoidosis, idiopathicpulmonary fibrosis by preventing the recruitment and activation ofmononuclear phagocytes. They may also be employed to treat, prevent,and/or diagnose idiopathic hyper-eosinophilic syndrome by preventingeosinophil production and migration. Endotoxic shock may also be treatedby the antagonists by preventing the migration of macrophages and theirproduction of the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the present invention. The antagonists may also beemployed for treating atherosclerosis, by preventing monocyteinfiltration in the artery wall. The antagonists may also be employed totreat, prevent, and/or diagnose histamine-mediated allergic reactionsand immunological disorders including late phase allergic reactions,chronic urticaria, and atopic dermatitis by inhibiting chemokine-inducedmast cell and basophil degranulation and release of histamine.IgE-mediated allergic reactions such as allergic asthma, rhinitis, andeczema may also be treated. The antagonists may also be employed totreat, prevent, and/or diagnose chronic and acute inflammation bypreventing the attraction of monocytes to a wound area. They may also beemployed to regulate normal pulmonary macrophage populations, sincechronic and acute inflammatory pulmonary diseases are associated withsequestration of mononuclear phagocytes in the lung. Antagonists mayalso be employed to treat, prevent, and/or diagnose rheumatoid arthritisby preventing the attraction of monocytes into synovial fluid in thejoints of patients. Monocyte influx and activation plays a significantrole in the pathogenesis of both degenerative and inflammatoryarthropathies. The antagonists may be employed to interfere with thedeleterious cascades attributed primarily to IL-1 and TNF, whichprevents the biosynthesis of other inflammatory cytokines. In this way,the antagonists may be employed to prevent inflammation. The antagonistsmay also be employed to inhibit prostaglandin-independent fever inducedby Neutrokine-alpha and/or Neutrokine-alphaSV. The antagonists may alsobe employed to treat, prevent, and/or diagnose cases of bone marrowfailure, for example, aplastic anemia and myelodysplastic syndrome. Theantagonists may also be employed to treat, prevent, and/or diagnoseasthma and allergy by preventing eosinophil accumulation in the lung.The antagonists may also be employed to treat, prevent, and/or diagnosesubepithelial basement membrane fibrosis which is a prominent feature ofthe asthmatic lung. The antagonists may also be employed to treat,prevent, and/or diagnose lymphomas (e.g., one or more of the extensive,but not limiting, list of lymphomas provided herein).

All of the above described applications as they may apply to veterinarymedicine. Moreover, all applications described herein may also apply toveterinary medicine.

Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention and/or agonists and/or antagoniststhereof, may be used to treat, prevent, and/or diagnose various immunesystem-related disorders and/or conditions associated with thesedisorders, in mammals, preferably humans. Many autoimmune disordersresult from inappropriate recognition of self as foreign material byimmune cells. This inappropriate recognition results in an immuneresponse leading to the destruction of the host tissue. Therefore, theadministration of Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides of the invention and/or agonists and/orantagonists thereof that can inhibit an immune response, particularlythe proliferation of B cells and/or the production of immunoglobulins,may be an effective therapy in treating and/or preventing autoimmunedisorders. Thus, in preferred embodiments, Neutrokine-alpha and/orNeutrokine-alphaSV antagonists of the invention (e.g., polypeptidefragments of Neutrokine-alpha and/or Neutrokine-alphaSV andanti-Neutrokine-alpha antibodies) are used to treat, prevent, and/ordiagnose an autoimmune disorder.

Autoimmune disorders and conditions associated with these disorders thatmay be treated, prevented, and/or diagnosed with the Neutrokine-alphapolynucleotides, polypeptides, and/or antagonist of the invention (e.g.,anti-Neutrokine-alpha antibodies), include, but are not limited to,autoimmune hemolytic anemia, autoimmune neonatal thrombocytopenia,idiopathic thrombocytopenia purpura, autoimmunocytopenia, hemolyticanemia, antiphospholipid syndrome, dermatitis, allergicencephalomyelitis, myocarditis, relapsing polychondritis, rheumaticheart disease, glomerulonephritis (e.g., IgA nephropathy), MultipleSclerosis, Neuritis, Uveitis Ophthalmia, Polyendocrinopathies, Purpura(e.g., Henloch-Scoenlein purpura), Reiter's Disease, Stiff-Man Syndrome,Autoimmune Pulmonary Inflammation, Guillain-Barre Syndrome, insulindependent diabetes mellitus, and autoimmune inflammatory eye disease.

Additional autoimmune disorders (that are highly probable) that may betreated, prevented, and/or diagnosed with the compositions of theinvention include, but are not limited to, autoimmune thyroiditis,hypothyroidism (i.e., Hashimoto's thyroiditis) (often characterized,e.g., by cell-mediated and humoral thyroid cytotoxicity), systemic lupuserythematosus (often characterized, e.g., by circulating and locallygenerated immune complexes), Goodpasture's syndrome (oftencharacterized, e.g., by anti-basement membrane antibodies), Pemphigus(often characterized, e.g., by epidermal acantholytic antibodies),Receptor autoimmunities such as, for example, (a) Graves' Disease (oftencharacterized, e.g., by TSH receptor antibodies), (b) Myasthenia Gravis(often characterized, e.g., by acetylcholine receptor antibodies), and(c) insulin resistance (often characterized, e.g., by insulin receptorantibodies), autoimmune hemolytic anemia (often characterized, e.g., byphagocytosis of antibody-sensitized RBCs), autoimmune thrombocytopenicpurpura (often characterized, e.g., by phagocytosis ofantibody-sensitized platelets.

Additional autoimmune disorders (that are probable) that may be treated,prevented, and/or diagnosed with the compositions of the inventioninclude, but are not limited to, rheumatoid arthritis (oftencharacterized, e.g., by immune complexes in joints), schleroderma withanti-collagen antibodies (often characterized, e.g., by nucleolar andother nuclear antibodies), mixed connective tissue disease (oftencharacterized, e.g., by antibodies to extractable nuclear antigens(e.g., ribonucleoprotein)), polymyositis/dermatomyositis (oftencharacterized, e.g., by nonhistone ANA), pernicious anemia (oftencharacterized, e.g., by antiparietal cell, microsomes, and intrinsicfactor antibodies), idiopathic Addison's disease (often characterized,e.g., by humoral and cell-mediated adrenal cytotoxicity, infertility(often characterized, e.g., by antispermatozoal antibodies),glomerulonephritis (often characterized, e.g., by glomerular basementmembrane antibodies or immune complexes) such as primaryglomerulonephritis and IgA nephropathy, bullous pemphigoid (oftencharacterized, e.g., by IgG and complement in basement membrane),Sjogren's syndrome (often characterized, e.g., by multiple tissueantibodies, and/or a specific nonhistone ANA (SS-B)), diabetes mellitus(often characterized, e.g., by cell-mediated and humoral islet cellantibodies), and adrenergic drug resistance (including adrenergic drugresistance with asthma or cystic fibrosis) (often characterized, e.g.,by beta-adrenergic receptor antibodies).

Additional autoimmune disorders (that are possible) that may be treated,prevented, and/or diagnosed with the compositions of the inventioninclude, but are not limited to, chronic active hepatitis (oftencharacterized, e.g., by smooth muscle antibodies), primary biliarycirrhosis (often characterized, e.g., by mitchondrial antibodies), otherendocrine gland failure (often characterized, e.g., by specific tissueantibodies in some cases), vitiligo (often characterized, e.g., bymelanocyte antibodies), vasculitis (often characterized, e.g., by Ig andcomplement in vessel walls and/or low serum complement), post-MI (oftencharacterized, e.g., by myocardial antibodies), cardiotomy syndrome(often characterized, e.g., by myocardial antibodies), urticaria (oftencharacterized, e.g., by IgG and IgM antibodies to IgE), atopicdermatitis (often characterized, e.g., by IgG and IgM antibodies toIgE), asthma (often characterized, e.g., by IgG and IgM antibodies toIgE), inflammatory myopathies, and many other inflammatory,granulomatous, degenerative, and atrophic disorders.

In a preferred embodiment, the autoimmune diseases and disorders and/orconditions associated with the diseases and disorders recited above aretreated, prevented, and/or diagnosed using anti-Neutrokine-alphaantibodies and/or anti-Neutrokine-alphaSV.

In a specific preferred embodiment, rheumatoid arthritis is treated,prevented, and/or diagnosed using anti-Neutrokine-alpha antibodiesand/or anti-Neutrokine-alphaSV antibodies and/or other antagonist of theinvention.

In a specific preferred embodiment, lupus is treated, prevented, and/ordiagnosed using anti-Neutrokine-alpha antibodies and/oranti-Neutrokine-alphaSV antibodies and/or other antagonist of theinvention.

In a specific preferred embodiment, nephritis associated with lupus istreated, prevented, and/or diagnosed using anti-Neutrokine-alphaantibodies and/or anti-Neutrokine-alphaSV antibodies and/or otherantagonist of the invention.

In a specific embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides, or antagonists thereof (e.g.,anti-Neutrokine-alpha and/or anti-Neutrokine-alphaSV antibodies) areused to treat or prevent systemic lupus erythematosus and/or diseases,disorders or conditions associated therewith. Lupus-associated diseases,disorders, or conditions that may be treated or prevented withNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides, or antagonists of the invention, include, but are notlimited to, hematologic disorders (e.g., hemolytic anemia, leukopenia,lymphopenia, and thrombocytopenia), immunologic disorders (e.g.,anti-DNA antibodies, and anti-Sm antibodies), rashes, photosensitivity,oral ulcers, arthritis, fever, fatigue, weight loss, serositis (e.g.,pleuritus (pleuricy)), renal disorders (e.g., nephritis), neurologicaldisorders (e.g., seizures, peripheral neuropathy, CNS relateddisorders), gastroinstestinal disorders, Raynaud phenomenon, andpericarditis. In a preferred embodiment, the Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides, or antagoniststhereof (e.g., anti-Neutrokine-alpha and/or anti-Neutrokine-alphaSVantibodies) are used to treat or prevent renal disorders associated withsystemic lupus erythematosus. In a most preferred embodiment,Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides, or antagonists thereof (e.g., anti-Neutrokine-alpha and/oranti-Neutrokine-alphaSV antibodies) are used to treat or preventnephritis associated with systemic lupus erythematosus.

Similarly, allergic reactions and conditions, such as asthma(particularly allergic asthma) or other respiratory problems, may alsobe treated by Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotidesor polypeptides of the invention and/or agonists and/or antagoniststhereof. Moreover, these molecules can be used to treat, prevent, and/ordiagnose anaphylaxis, hypersensitivity to an antigenic molecule, orblood group incompatibility.

Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention and/or agonists and/or antagoniststhereof, may also be used to treat, prevent, and/or diagnose organrejection or graft-versus-host disease (GVHD) and/or conditionsassociated therewith. Organ rejection occurs by host immune celldestruction of the transplanted tissue through an immune response.Similarly, an immune response is also involved in GVHD, but, in thiscase, the foreign transplanted immune cells destroy the host tissues.The administration of Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides of the invention and/or agonists and/orantagonists thereof, that inhibit an immune response, particularly theproliferation, differentiation, or chemotaxis of T-cells, may be aneffective therapy in preventing organ rejection or GVHD.

Similarly, Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention and/or agonists and/or antagoniststhereof, may also be used to modulate inflammation. For example,Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention and/or agonists and/or antagoniststhereof, may inhibit the proliferation and differentiation of cellsinvolved in an inflammatory response. These molecules can be used totreat, prevent, and/or diagnose inflammatory conditions, both chronicand acute conditions, including chronic prostatitis, granulomatousprostatitis and malacoplakia, inflammation associated with infection(e.g., septic shock, sepsis, or systemic inflammatory response syndrome(SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis,complement-mediated hyperacute rejection, nephritis, cytokine orchemokine induced lung injury, inflammatory bowel disease, Crohn'sdisease, or resulting from over production of cytokines (e.g., TNF orIL-1.)

In a specific embodiment, anti-Neutrokine-alpha antibodies and/oranti-Neutrokine-alphaSV antibodies of the invention are used to treat,prevent, modulate, detect, and/or diagnose inflammation.

In a specific embodiment, anti-Neutrokine-alpha antibodies and/oranti-Neutrokine-alphaSV antibodies of the invention are used to treat,prevent, modulate, detect, and/or diagnose inflammatory disorders.

In another specific embodiment, anti-Neutrokine-alpha antibodies and/oranti-Neutrokine-alphaSV antibodies of the invention are used to treat,prevent, modulate, detect, and/or diagnose allergy and/orhypersensitivity.

Antibodies against Neutrokine-alpha and/or Neutrokine-alphaSV may beemployed to bind to and inhibit Neutrokine-alpha and/orNeutrokine-alphaSV activity to treat, prevent, and/or diagnose ARDS, bypreventing infiltration of neutrophils into the lung after injury. Theagonists and antagonists of the instant may be employed in a compositionwith a pharmaceutically acceptable carrier, e.g., as describedhereinafter.

Neutrokine-alpha and/or Neutrokine-alphaSV and/or Neutrokine-alphareceptor polynucleotides or polypeptides of the invention and/oragonists and/or antagonists thereof, are used to treat, prevent, and/ordiagnose diseases and disorders of the pulmonary system (e.g., bronchisuch as, for example, sinopulmonary and bronchial infections andconditions associated with such diseases and disorders and otherrespiratory diseases and disorders. In specific embodiments, suchdiseases and disorders include, but are not limited to, bronchialadenoma, bronchial asthma, pneumonia (such as, e.g., bronchialpneumonia, bronchopneumonia, and tuberculous bronchopneumonia), chronicobstructive pulmonary disease (COPD), bronchial polyps, bronchiectasia(such as, e.g., bronchiectasia sicca, cylindrical bronchiectasis, andsaccular bronchiectasis), bronchiolar adenocarcinoma, bronchiolarcarcinoma, bronchiolitis (such as, e.g., exudative bronchiolitis,bronchiolitis fibrosa obliterans, and proliferative bronchiolitis),bronchiolo-alveolar carcinoma, bronchitic asthma, bronchitis (such as,e.g., asthmatic bronchitis, Castellani's bronchitis, chronic bronchitis,croupous bronchitis, fibrinous bronchitis, hemorrhagic bronchitis,infectious avian bronchitis, obliterative bronchitis, plasticbronchitis, pseudomembranous bronchitis, putrid bronchitis, andverminous bronchitis), bronchocentric granulomatosis, bronchoedema,bronchoesophageal fistula, bronchogenic carcinoma, bronchogenic cyst,broncholithiasis, bronchomalacia, bronchomycosis (such as, e.g.,bronchopulmonary aspergillosis), bronchopulmonary spirochetosis,hemorrhagic bronchitis, bronchorrhea, bronchospasm, bronchostaxis,bronchostenosis, Biot's respiration, bronchial respiration, Kussmaulrespiration, Kussmaul-Kien respiration, respiratory acidosis,respiratory alkalosis, respiratory distress syndrome of the newborn,respiratory insufficiency, respiratory scleroma, respiratory syncytialvirus, and the like.

In a specific embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides of the invention and/or agonists and/orantagonists thereof, are used to treat, prevent, and/or diagnose chronicobstructive pulmonary disease (COPD).

In another embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides of the invention and/or agonists and/orantagonists thereof, are used to treat, prevent, and/or diagnosefibroses and conditions associated with fibroses, such as, for example,but not limited to, cystic fibrosis (including such fibroses as cysticfibrosis of the pancreas, Clarke-Hadfield syndrome, fibrocystic diseaseof the pancreas, mucoviscidosis, and viscidosis), endomyocardialfibrosis, idiopathic retroperitoneal fibrosis, leptomeningeal fibrosis,mediastinal fibrosis, nodular subepidermal fibrosis, pericentralfibrosis, perimuscular fibrosis, pipestem fibrosis, replacementfibrosis, subadventitial fibrosis, and Symmers' clay pipestem fibrosis.

The TNF family ligands are known to be among the most pleiotropiccytokines, inducing a large number of cellular responses, includingcytotoxicity, anti-viral activity, immunoregulatory activities, and thetranscriptional regulation of several genes (D. V. Goeddel et al.,“Tumor Necrosis Factors: Gene Structure and Biological Activities,”Symp. Quant. Biol. 51:597-609 (1986), Cold Spring Harbor; B. Beutler andA. Cerami, Annu. Rev. Biochem. 57:505-518 (1988); L. J. Old, Sci. Am.258:59-75 (1988); W. Fiers, FEBS Lett. 285:199-224 (1991)). TheTNF-family ligands, including Neutrokine-alpha and/or Neutrokine-alphaSVof the present invention, induce such various cellular responses bybinding to TNF-family receptors. Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides are believed to elicit a potent cellularresponse including any genotypic, phenotypic, and/or morphologic changeto the cell, cell line, tissue, tissue culture or patient. As indicated,such cellular responses include not only normal physiological responsesto TNF-family ligands, but also diseases associated with increasedapoptosis or the inhibition of apoptosis. Apoptosis—programmed celldeath—is a physiological mechanism involved in the deletion ofperipheral B and/or T lymphocytes of the immune system, and itsdisregulation can lead to a number of different pathogenic processes (J.C. Ameisen, AIDS 8:1197-1213 (1994); P. H. Krammer et al., Curr. Opin.Immunol. 6:279-289 (1994)).

Diseases associated with increased cell survival, or the inhibition ofapoptosis that may be diagnosed, treated, or prevented with theNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention, and agonists and antagonists thereof,include cancers (such as follicular lymphomas, carcinomas with p53mutations, and hormone-dependent tumors, including, but not limited to,colon cancer, cardiac tumors, pancreatic cancer, melanoma,retinoblastoma, glioblastoma, lung cancer, intestinal cancer, testicularcancer, stomach cancer, neuroblastoma, myxoma, myoma, lymphoma,endothelioma, osteoblastoma, osteoclastoma, osteosarcoma,chondrosarcoma, adenoma, breast cancer, prostate cancer, Kaposi'ssarcoma and ovarian cancer); autoimmune disorders (such as systemiclupus erythematosus and immune-related glomerulonephritis rheumatoidarthritis); viral infections (such as herpes viruses, pox viruses andadenoviruses); inflammation; graft vs. host disease; acute graftrejection and chronic graft rejection. Thus, in preferred embodimentsNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention and/or agonists or antagonists thereof,are used to treat, prevent, and/or diagnose autoimmune diseases and/orinhibit the growth, progression, and/or metastasis of cancers,including, but not limited to, those cancers disclosed herein, such as,for example, lymphocytic leukemias (including, for example, MLL andchronic lymphocytic leukemia (CLL)) and follicular lymphomas. In anotherembodiment, Neutrokine-alpha and/or Neutrokine-alphaSV polynucleotidesor polypeptides of the invention are used to activate, differentiate orproliferate cancerous cells or tissue (e.g., B cell lineage relatedcancers (e.g., CLL and MLL), lymphocytic leukemia, or lymphoma) andthereby render the cells more vulnerable to cancer therapy (e.g.,chemotherapy or radiation therapy).

Moreover, in other embodiments, Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides of the invention oragonists or antagonists thereof, are used to inhibit the growth,progression, and/or metastases of malignancies and related disorderssuch as leukemia (including acute leukemias (e.g., acute lymphocyticleukemia, acute myelocytic leukemia (including myeloblastic,promyelocytic, myelomonocytic, monocytic, and erythroleukemia)) andchronic leukemias (e.g., chronic myelocytic (granulocytic) leukemia andchronic lymphocytic leukemia)), polycythemia vera, lymphomas (e.g.,Hodgkin's disease and non-Hodgkin's disease), multiple myeloma,Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumorsincluding, but not limited to, sarcomas and carcinomas such asfibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenicsarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma,lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor,leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer,breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma,basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceousgland carcinoma, papillary carcinoma, papillary adenocarcinomas,cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renalcell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma,seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, testiculartumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma,epithelial carcinoma, glioma, astrocytoma, medulloblastoma,craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acousticneuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma, andretinoblastoma.

Diseases associated with increased apoptosis that may be diagnosed,treated, or prevented with the Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides of the invention, andagonists and antagonists thereof, include AIDS; neurodegenerativedisorders (such as Alzheimer's disease, Parkinson's disease, Amyotrophiclateral sclerosis, Retinitis pigmentosa, Cerebellar degeneration);myelodysplastic syndromes (such as aplastic anemia), ischemic injury(such as that caused by myocardial infarction, stroke and reperfusioninjury), toxin-induced liver disease (such as that caused by alcohol),septic shock, cachexia and anorexia. Thus, in preferred embodimentsNeutrokine-alpha and/or Neutrokine-alphaSV polynucleotides orpolypeptides of the invention and/or agonists or antagonists thereof,are used to treat, prevent, and/or diagnose the diseases and disorderslisted above.

In preferred embodiments, Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the invention and/or agonists or antagonists thereof(e.g., anti-Neutrokine-alpha antibodies) inhibit the growth of humanhistiocytic lymphoma U-937 cells in a dose-dependent manner. Inadditional preferred embodiments, Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention and/or agonists orantagonists thereof (e.g., anti-Neutrokine-alpha antibodies) inhibit thegrowth of PC-3 cells, HT-29 cells, HeLa cells, MCF-7 cells, and A293cells. In highly preferred embodiments, Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotides or polypeptides of the inventionand/or agonists or antagonists thereof (e.g., anti-Neutrokine-alphaantibodies) are used to inhibit growth, progression, and/or metastasisof prostate cancer, colon cancer, cervical carcinoma, and breastcarcinoma.

Thus, in additional preferred embodiments, the present invention isdirected to a method for enhancing apoptosis induced by a TNF-familyligand, which involves administering to a cell which expresses aNeutrokine-alpha and/or Neutrokine-alphaSV receptor an effective amountof Neutrokine-alpha and/or Neutrokine-alphaSV, or an agonist orantagonist thereof, capable of increasing or decreasing Neutrokine-alphaand/or Neutrokine-alphaSV mediated signaling. Preferably,Neutrokine-alpha and/or Neutrokine-alphaSV mediated signaling isincreased or decreased to treat, prevent, and/or diagnose a diseasewherein decreased apoptosis or decreased cytokine and adhesion moleculeexpression is exhibited. An agonist or antagonist can include solubleforms of Neutrokine-alpha and/or Neutrokine-alphaSV and monoclonalantibodies directed against the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide.

In a further aspect, the present invention is directed to a method forinhibiting apoptosis induced by a TNF-family ligand, which involvesadministering to a cell which expresses the Neutrokine-alpha and/orNeutrokine-alphaSV receptor an effective amount of an agonist orantagonist capable of increasing or decreasing Neutrokine-alpha and/orNeutrokine-alphaSV mediated signaling. Preferably, Neutrokine-alphaand/or Neutrokine-alphaSV mediated signaling is increased or decreasedto treat, prevent, and/or diagnose a disease wherein increased apoptosisor NF-kappaB expression is exhibited. An agonist or antagonist caninclude soluble forms of Neutrokine-alpha and/or Neutrokine-alphaSV andmonoclonal antibodies directed against the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide.

Because Neutrokine-alpha and/or Neutrokine-alphaSV belong to the TNFsuperfamily, the polypeptides should also modulate angiogenesis. Inaddition, since Neutrokine-alpha and/or Neutrokine-alphaSV inhibitimmune cell functions, the polypeptides will have a wide range ofanti-inflammatory activities. Neutrokine-alpha and/or Neutrokine-alphaSVmay be employed as an anti-neovascularizing agent to treat, prevent,and/or diagnose solid tumors by stimulating the invasion and activationof host defense cells, e.g., cytotoxic T cells and macrophages and byinhibiting the angiogenesis of tumors. Those of skill in the art willrecognize other non-cancer indications where blood vessel proliferationis not wanted. They may also be employed to enhance host defensesagainst resistant chronic and acute infections, for example,myobacterial infections via the attraction and activation ofmicrobicidal leukocytes. Neutrokine-alpha and/or Neutrokine-alphaSV mayalso be employed to inhibit T-cell proliferation by the inhibition ofIL-2 biosynthesis for the treatment of T-cell mediated auto-immunediseases and lymphocytic leukemias (including, for example, chroniclymphocytic leukemia (CLL)). Neutrokine-alpha and/or Neutrokine-alphaSVmay also be employed to stimulate wound healing, both via therecruitment of debris clearing and connective tissue promotinginflammatory cells. In this same manner, Neutrokine-alpha and/orNeutrokine-alphaSV may also be employed to treat, prevent, and/ordiagnose other fibrotic disorders, including liver cirrhosis,osteoarthritis and pulmonary fibrosis. Neutrokine-alpha and/orNeutrokine-alphaSV also increases the presence of eosinophils that havethe distinctive function of killing the larvae of parasites that invadetissues, as in schistosomiasis, trichinosis and ascariasis. It may alsobe employed to regulate hematopoiesis, by regulating the activation anddifferentiation of various hematopoietic progenitor cells, for example,to release mature leukocytes from the bone marrow followingchemotherapy, i.e., in stem cell mobilization. Neutrokine-alpha and/orNeutrokine-alphaSV may also be employed to treat, prevent, and/ordiagnose sepsis.

Polynucleotides and/or polypeptides of the invention and/or agonistsand/or antagonists thereof are useful in the diagnosis and treatment orprevention of a wide range of diseases and/or conditions. Such diseasesand conditions include, but are not limited to, cancer (e.g., immunecell related cancers, breast cancer, prostate cancer, ovarian cancer,follicular lymphoma, cancer associated with mutation or alteration ofp53, brain tumor, bladder cancer, uterocervical cancer, colon cancer,colorectal cancer, non-small cell carcinoma of the lung, small cellcarcinoma of the lung, stomach cancer, etc.), lymphoproliferativedisorders (e.g., lymphadenopathy), microbial (e.g., viral, bacterial,etc.) infection (e.g., HIV-1 infection, HIV-2 infection, herpesvirusinfection (including, but not limited to, HSV-1, HSV-2, CMV, VZV, HHV-6,HHV-7, EBV), adenovirus infection, poxvirus infection, human papillomavirus infection, hepatitis infection (e.g., HAV, HBV, HCV, etc.),Helicobacter pylori infection, invasive Staphylococcia, etc.), parasiticinfection, nephritis, bone disease (e.g., osteoporosis),atherosclerosis, pain, cardiovascular disorders (e.g.,neovascularization, hypovascularization or reduced circulation (e.g.,ischemic disease (e.g., myocardial infarction, stroke, etc.)), AIDS,allergy, inflammation, neurodegenerative disease (e.g., Alzheimer'sdisease, Parkinson's disease, amyotrophic lateral sclerosis, pigmentaryretinitis, cerebellar degeneration, etc.), graft rejection (acute andchronic), graft vs. host disease, diseases due to osteomyelodysplasia(e.g., aplastic anemia, etc.), joint tissue destruction in rheumatism,liver disease (e.g., acute and chronic hepatitis, liver injury, andcirrhosis), autoimmune disease (e.g., multiple sclerosis, rheumatoidarthritis, systemic lupus erythematosus, immune complexglomerulonephritis, autoimmune diabetes, autoimmune thrombocytopenicpurpura, Grave's disease, Hashimoto's thyroiditis, etc.), cardiomyopathy(e.g., dilated cardiomyopathy), diabetes, diabetic complications (e.g.,diabetic nephropathy, diabetic neuropathy, diabetic retinopathy),influenza, asthma, psoriasis, glomerulonephritis, septic shock, andulcerative colitis.

Polynucleotides and/or polypeptides of the invention and/or agonistsand/or antagonists thereof are useful in promoting angiogenesis, woundhealing (e.g., wounds, burns, and bone fractures). Polynucleotidesand/or polypeptides of the invention and/or agonists and/or antagoniststhereof are also useful as an adjuvant to enhance immune responsivenessto specific antigen, anti-viral immune responses.

More generally, polynucleotides and/or polypeptides of the inventionand/or agonists and/or antagonists thereof are useful in regulating(i.e., elevating or reducing) immune response. For example,polynucleotides and/or polypeptides of the invention may be useful inpreparation or recovery from surgery, trauma, radiation therapy,chemotherapy, and transplantation, or may be used to boost immuneresponse and/or recovery in the elderly and immunocompromisedindividuals. Alternatively, polynucleotides and/or polypeptides of theinvention and/or agonists and/or antagonists thereof are useful asimmunosuppressive agents, for example in the treatment or prevention ofautoimmune disorders. In specific embodiments, polynucleotides and/orpolypeptides of the invention are used to treat or prevent chronicinflammatory, allergic or autoimmune conditions, such as those describedherein or are otherwise known in the art.

Preferably, treatment using Neutrokine-alpha and/or Neutrokine-alphaSVpolynucleotides or polypeptides, and/or agonists or antagonists ofNeutrokine-alpha and/or Neutrokine-alphaSV (e.g., anti-Neutrokine-alphaantibody), could either be by administering an effective amount ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide of the invention,or agonist or antagonist thereof, to the patient, or by removing cellsfrom the patient, supplying the cells with Neutrokine-alpha and/orNeutrokine-alphaSV polynucleotide, and returning the engineered cells tothe patient (ex vivo therapy). Moreover, as further discussed herein,the Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide orpolynucleotide can be used as an adjuvant in a vaccine to raise animmune response against infectious disease.

Formulations and Administration

The Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide composition(preferably containing a polypeptide which is a soluble form of theNeutrokine-alpha and/or Neutrokine-alphaSV extracellular domains) willbe formulated and dosed in a fashion consistent with good medicalpractice, taking into account the clinical condition of the individualpatient (especially the side effects of treatment with Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide alone), the site of delivery ofthe Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide composition,the method of administration, the scheduling of administration, andother factors known to practitioners. The “effective amount” ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide for purposesherein is thus determined by such considerations.

As a general proposition, the total pharmaceutically effective amount ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide administeredparenterally per dose will be in the range of about 1 microgram/kg/dayto 10 mg/kg/day of patient body weight, although, as noted above, thiswill be subject to therapeutic discretion. More preferably, this dose isat least 0.01 mg/kg/day, and most preferably for humans between about0.01 and 1 mg/kg/day.

In another embodiment, the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide of the invention is administered to a human at a dosebetween 0.0001 and 0.045 mg/kg/day, preferably, at a dose between 0.0045and 0.045 mg/kg/day, and more preferably, at a dose of about 45microgram/kg/day in humans; and at a dose of about 3 mg/kg/day in mice.

If given continuously, the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide is typically administered at a dose rate of about 1microgram/kg/hour to about 50 micrograms/kg/hour, either by 1-4injections per day or by continuous subcutaneous infusions, for example,using a mini-pump. An intravenous bag solution may also be employed.

The length of treatment needed to observe changes and the intervalfollowing treatment for responses to occur appears to vary depending onthe desired effect.

In a specific embodiment, the total pharmaceutically effective amount ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide administeredparenterally per dose will be in the range of about 0.1 microgram/kg/dayto 45 micrograms/kg/day of patient body weight, although, as notedabove, this will be subject to therapeutic discretion. More preferably,this dose is at least 0.1 microgram/kg/day, and most preferably forhumans between about 0.01 and 50 micrograms/kg/day for the protein.Neutrokine-alpha and/or Neutrokine-alphaSV may be administered as acontinuous infusion, multiple discrete injections per day (e.g., threeor more times daily, or twice daily), single injection per day, or asdiscrete injections given intermitently (e.g., twice daily, once daily,every other day, twice weekly, weekly, biweekly, monthly, bimonthly, andquarterly). If given continuously, the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide is typically administered at a dose rateof about 0.001 to 10 microgram/kg/hour to about 50 micrograms/kg/hour,either by 1-4 injections per day or by continuous subcutaneousinfusions, for example, using a mini-pump.

Effective dosages of the compositions of the present invention to beadministered may be determined through procedures well known to those inthe art which address such parameters as biological half-life,bioavailability, and toxicity. Such determination is well within thecapability of those skilled in the art, especially in light of thedetailed disclosure provided herein.

Bioexposure of an organism to Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide during therapy may also play an important role indetermining a therapeutically and/or pharmacologically effective dosingregime. Variations of dosing such as repeated administrations of arelatively low dose of Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide for a relatively long period of time may have an effectwhich is therapeutically and/or pharmacologically distinguishable fromthat achieved with repeated administrations of a relatively high dose ofNeutrokine-alpha and/or Neutrokine-alphaSV for a relatively short periodof time. See, for instance, the serum immunoglobulin level experimentspresented in Example 6.

Using the equivalent surface area dosage conversion factors supplied byFreireich, E. J., et al. (Cancer Chemotherapy Reports 50(4):219-44(1966)), one of ordinary skill in the art is able to convenientlyconvert data obtained from the use of Neutrokine-alpha and/orNeutrokine-alphaSV in a given experimental system into an accurateestimation of a pharmaceutically effective amount of Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide to be administered per dose inanother experimental system. Experimental data obtained through theadministration of Neutrokine-alpha in mice (see, for instance, Example6) may converted through the conversion factors supplied by Freireich,et al., to accurate estimates of pharmaceutically effective doses ofNeutrokine-alpha in rat, monkey, dog, and human. The followingconversion table (Table III) is a summary of the data provided byFreireich, et al. Table III gives approximate factors for convertingdoses expressed in terms of mg/kg from one species to an equivalentsurface area dose expressed as mg/kg in another species tabulated.

TABLE III Equivalent Surface Area Dosage Conversion Factors. --TO--Mouse Rat Monkey --FROM-- (20 g) (150 g) (3.5 kg) (8 kg) Dog (60 kg)Human Mouse 1 1/2 1/4 1/6  1/12 Rat 2 1 1/2 1/4 1/7 Monkey 4 2 1 3/5 1/3Dog 6 4 5/3 1 1/2 Human 12 7 3 2 1

Thus, for example, using the conversion factors provided in Table III, adose of 50 mg/kg in the mouse converts to an appropriate dose of 12.5mg/kg in the monkey because (50 mg/kg)×(¼)=12.5 mg/kg. As an additionalexample, doses of 0.02, 0.08, 0.8, 2, and 8 mg/kg in the mouse equate toeffect doses of 1.667 micrograms/kg, 6.67 micrograms/kg, 66.7micrograms/kg, 166.7 micrograms/kg, and 0.667 mg/kg, respectively, inthe human.

Pharmaceutical compositions containing Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention may be administeredorally, rectally, parenterally, subcutaneously, intracistemally,intravaginally, intraperitoneally, topically (as by powders, ointments,drops or transdermal patch), bucally, or as an oral or nasal spray(e.g., via inhalation of a vapor or powder). In one embodiment,“pharmaceutically acceptable carrier” means a non-toxic solid, semisolidor liquid filler, diluent, encapsulating material or formulationauxiliary of any type. In a specific embodiment, “pharmaceuticallyacceptable” means approved by a regulatory agency of the federal or astate government or listed in the U.S. Pharmacopeia or other generallyrecognized pharmacopeia for use in animals, and more particularlyhumans. Nonlimiting examples of suitable pharmaceutical carriersaccording to this embodiment are provided in “Remington's PharmaceuticalSciences” by E. W. Martin, and include sterile liquids, such as waterand oils, including those of petroleum, animal, vegetable or syntheticorigin, such as peanut oil, soybean oil, mineral oil, sesame oil and thelike. Water is a preferred carrier when the pharmaceutical compositionis administered intravenously. Saline solutions and aqueous dextrose andglycerol solutions can be employed as liquid carriers, particularly forinjectable solutions. The composition, if desired, can also containminor amounts of wetting or emulsifying agents, or pH buffering agents.These compositions can take the form of solutions, suspensions,emulsion, tablets, pills, capsules, powders, sustained-releaseformulations and the like.

The term “parenteral” as used herein refers to modes of administrationwhich include intravenous, intramuscular, intraperitoneal, intrasternal,subcutaneous and intraarticular injection and infusion.

In a preferred embodiment, Neutrokine-alpha and/or Neutrokine-alphaSVcompositions of the invention (including polypeptides, polynucleotides,and antibodies, and agonists and/or antagonists thereof) areadministered subcutaneously.

In another preferred embodiment, Neutrokine-alpha and/orNeutrokine-alphaSV compositions of the invention (includingpolypeptides, polynucleotides, and antibodies, and agonists and/orantagonists thereof) are administered intravenously.

Neutrokine-alpha and/or Neutrokine-alphaSV compositions of the inventionare also suitably administered by sustained-release systems. Suitableexamples of sustained-release compositions include suitable polymericmaterials (such as, for example, semi-permeable polymer matrices in theform of shaped articles, e.g., films, or microcapsules), suitablehydrophobic materials (for example as an emulsion in an acceptable oil)or ion exchange resins, and sparingly soluble derivatives (such as, forexample, a sparingly soluble salt).

Sustained-release matrices include polylactides (U.S. Pat. No.3,773,919, EP 58,481), copolymers of L-glutamic acid andgamma-ethyl-L-glutamate (Sidman, U. et al., Biopolymers 22:547-556(1983)), poly(2-hydroxyethyl methacrylate) (R. Langer et al., J. Biomed.Mater. Res. 15:167-277 (1981), and R. Langer, Chem. Tech. 12:98-105(1982)), ethylene vinyl acetate (R. Langer et al., Id.) orpoly-D-(−)-3-hydroxybutyric acid (EP 133,988).

Sustained-release compositions also include liposomally entrappedcompositions of the invention (see generally, Langer, Science249:1527-1533 (1990); Treat et al., in Liposomes in the Therapy ofInfectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss,New York, pp. 317-327 and 353-365 (1989)). Liposomes containingNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide may be preparedby methods known per se: DE 3,218,121; Epstein et al., Proc. Natl. Acad.Sci. (USA) 82:3688-3692 (1985); Hwang et al., Proc. Natl. Acad. Sci.(USA) 77:4030-4034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949;EP 142,641; Japanese Pat. Appl. 83-118008; U.S. Pat. Nos. 4,485,045 and4,544,545; and EP 102,324. Ordinarily, the liposomes are of the small(about 200-800 Angstroms) unilamellar type in which the lipid content isgreater than about 30 mol. percent cholesterol, the selected proportionbeing adjusted for the optimal Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide therapy.

In another embodiment sustained release compositions of the inventioninclude crystal formulations known in the art.

In yet an additional embodiment, the compositions of the invention aredelivered by way of a pump (see Langer, supra; Sefton, CRC Crit. Ref.Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980);Saudek et al., N. Engl. J. Med. 321:574 (1989)).

Other controlled release systems are discussed in the review by Langer(Science 249:1527-1533 (1990)).

For parenteral administration, in one embodiment, the Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide is formulated generally by mixingit at the desired degree of purity, in a unit dosage injectable form(solution, suspension, or emulsion), with a pharmaceutically acceptablecarrier, i.e., one that is non-toxic to recipients at the dosages andconcentrations employed and is compatible with other ingredients of theformulation. For example, the formulation preferably does not includeoxidizing agents and other compounds that are known to be deleterious topolypeptides.

Generally, the formulations are prepared by contacting theNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide uniformly andintimately with liquid carriers or finely divided solid carriers orboth. Then, if necessary, the product is shaped into the desiredformulation. Preferably the carrier is a parenteral carrier, morepreferably a solution that is isotonic with the blood of the recipient.Examples of such carrier vehicles include water, saline, Ringer'ssolution, and dextrose solution. Non-aqueous vehicles such as fixed oilsand ethyl oleate are also useful herein, as well as liposomes.

The carrier suitably contains minor amounts of additives such assubstances that enhance isotonicity and chemical stability. Suchmaterials are non-toxic to recipients at the dosages and concentrationsemployed, and include buffers such as phosphate, citrate, succinate,acetic acid, and other organic acids or their salts; antioxidants suchas ascorbic acid; low molecular weight (less than about ten residues)polypeptides, e.g., polyarginine or tripeptides; proteins, such as serumalbumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids, such as glycine, glutamic acid,aspartic acid, or arginine; monosaccharides, disaccharides, and othercarbohydrates including cellulose or its derivatives, glucose, manose,sucrose, or dextrins; chelating agents such as EDTA; sugar alcohols suchas mannitol or sorbitol; counterions such as sodium; preservatives, suchas cresol, phenol, chlorobutanol, benzyl alcohol and parabens, and/ornonionic surfactants such as polysorbates, poloxamers, or PEG.

The Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide is typicallyformulated in such vehicles at a concentration of about 0.001 mg/ml to100 mg/ml, or 0.1 mg/ml to 100 mg/ml, preferably 1-10 mg/ml or 1-10mg/ml, at a pH of about 3 to 10, or 3 to 8, more preferably 5-8, mostpreferably 6-7. It will be understood that the use of certain of theforegoing excipients, carriers, or stabilizers will result in theformation of Neutrokine-alpha and/or Neutrokine-alphaSV polypeptidesalts.

Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide to be used fortherapeutic administration must be sterile. Sterility is readilyaccomplished by filtration through sterile filtration membranes (e.g.,0.2 micron membranes). Therapeutic Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide compositions generally are placed into acontainer having a sterile access port, for example, an intravenoussolution bag or vial having a stopper pierceable by a hypodermicinjection needle.

Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide ordinarily willbe stored in unit or multi-dose containers, for example, sealed ampoulesor vials, as an aqueous solution or as a lyophilized formulation forreconstitution. As an example of a lyophilized formulation, 10-ml vialsare filled with 5 ml of sterile-filtered 1% (w/v) aqueousNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide solution, and theresulting mixture is lyophilized. The infusion solution is prepared byreconstituting the lyophilized Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide using bacteriostatic Water-for-Injection.

Alternatively, Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide isstored in single dose containers in lyophilized form. The infusionselection is reconstituted using a sterile carrier for injection.

The invention also provides a pharmaceutical pack or kit comprising oneor more containers filled with one or more of the ingredients of thepharmaceutical compositions of the invention. Optionally, associatedwith such container(s) is a notice in the form prescribed by agovernmental agency regulating the manufacture, use or sale ofpharmaceuticals or biological products, which notice reflects approvalby the agency of manufacture, use or sale for human administration. Inaddition, the polypeptides of the present invention may be employed inconjunction with other therapeutic compounds.

The compositions of the invention may be administered alone or incombination with other adjuvants. Adjuvants that may be administeredwith the compositions of the invention include, but are not limited to,alum, alum plus deoxycholate (ImmunoAg), MTP-PE (Biocine Corp.), QS21(Genentech, Inc.), BCG, and MPL. In a specific embodiment, compositionsof the invention are administered in combination with alum. In anotherspecific embodiment, compositions of the invention are administered incombination with QS-21. Further adjuvants that may be administered withthe compositions of the invention include, but are not limited to,Monophosphoryl lipid immunomodulator, AdjuVax 100a, QS-21, QS-18,CRL1005, Aluminum salts, MF-59, and Virosomal adjuvant technology.Vaccines that may be administered with the compositions of the inventioninclude, but are not limited to, vaccines directed toward protectionagainst MMR (measles, mumps, rubella), polio, varicella,tetanus/diptheria, hepatitis A, hepatitis B, haemophilus influenzae B,whooping cough, pneumonia, influenza, Lyme's Disease, rotavirus,cholera, yellow fever, Japanese encephalitis, poliomyelitis, rabies,typhoid fever, and pertussis, and/or PNEUMOVAX-23™. Combinations may beadministered either concomitantly, e.g., as an admixture, separately butsimultaneously or concurrently; or sequentially. This includespresentations in which the combined agents are administered together asa therapeutic mixture, and also procedures in which the combined agentsare administered separately but simultaneously, e.g., as throughseparate intravenous lines into the same individual. Administration “incombination” further includes the separate administration of one of thecompounds or agents given first, followed by the second.

In another specific embodiment, compositions of the invention are usedin combination with PNEUMOVAX-23™ to treat, prevent, and/or diagnoseinfection and/or any disease, disorder, and/or condition associatedtherewith. In one embodiment, compositions of the invention are used incombination with PNEUMOVAX-23™ to treat, prevent, and/or diagnose anyGram positive bacterial infection and/or any disease, disorder, and/orcondition associated therewith. In another embodiment, compositions ofthe invention are used in combination with PNEUMOVAX-23™ to treat,prevent, and/or diagnose infection and/or any disease, disorder, and/orcondition associated with one or more members of the genus Enterococcusand/or the genus Streptococcus. In another embodiment, compositions ofthe invention are used in any combination with PNEUMOVAX-23™ to treat,prevent, and/or diagnose infection and/or any disease, disorder, and/orcondition associated with one or more members of the Group Bstreptococci. In another embodiment, compositions of the invention areused in combination with PNEUMOVAX-23™ to treat, prevent, and/ordiagnose infection and/or any disease, disorder, and/or conditionassociated with Streptococcus pneumoniae.

The compositions of the invention may be administered alone or incombination with other therapeutic agents, including but not limited to,chemotherapeutic agents, antibiotics, antivirals, steroidal andnon-steroidal anti-inflammatories, conventional immunotherapeutic agentsand cytokines. Combinations may be administered either concomitantly,e.g., as an admixture, separately but simultaneously or concurrently; orsequentially. This includes presentations in which the combined agentsare administered together as a therapeutic mixture, and also proceduresin which the combined agents are administered separately butsimultaneously, e.g., as through separate intravenous lines into thesame individual. Administration “in combination” further includes theseparate administration of one of the compounds or agents given first,followed by the second.

In one embodiment, the compositions of the invention are administered incombination with other members of the TNF family. TNF, TNF-related orTNF-like molecules that may be administered with the compositions of theinvention include, but are not limited to, soluble forms of TNF-alpha,lymphotoxin-alpha (LT-alpha, also known as TNF-beta), LT-beta (found incomplex heterotrimer LT-alpha2-beta), OPGL, FasL, CD27L, CD30L, CD40L,4-1BBL, DcR3, OX40L, TNF-gamma (International Publication No. WO96/14328), AIM-I (International Publication No. WO 97/33899), AIM-II(International Publication No. WO 97/34911), APRIL (J. Exp. Med.188(6):1185-1190), endokine-alpha (International Publication No. WO98/07880), TR6 (International Publication No. WO 98/30694), OPG, andneutrokine-alpha (International Publication No. WO 98/18921, OX40, andnerve growth factor (NGF), and soluble forms of Fas, CD30, CD27, CD40and 4-IBB, TR2 (International Publication No. WO 96/34095), DR3(International Publication No. WO 97/33904), DR4 (InternationalPublication No. WO 98/32856), TR5 (International Publication No. WO98/30693), TR6 (International Publication No. WO 98/30694), TR7(International Publication No. WO 98/41629), TRANK, TR9 (InternationalPublication No. WO 98/56892), TR10 (International Publication No. WO98/54202), 312C2 (International Publication No. WO 98/06842), and TR12.

In a preferred embodiment, the compositions of the invention areadministered in combination with CD40 ligand (CD40L), a soluble form ofCD40L (e.g., AVREND™) biologically active fragments, variants, orderivatives of CD40L, anti-CD40L antibodies (e.g., agonistic orantagonistic antibodies), and/or anti-CD40 antibodies (e.g., agonisticor antagonistic antibodies).

In certain embodiments, compositions of the invention are administeredin combination with antiretroviral agents, nucleoside reversetranscriptase inhibitors, non-nucleoside reverse transcriptaseinhibitors, and/or protease inhibitors. Nucleoside reverse transcriptaseinhibitors that may be administered in combination with the compositionsof the invention, include, but are not limited to, RETROVIR™(zidovudine/AZT), VIDEX™ (didanosine/ddI), HIVID™ (zalcitabine/ddC),ZERIT™ (stavudine/d4T), EPIVIR™ (lamivudine/3TC), and COMBIVIR™(zidovudine/lamivudine). Non-nucleoside reverse transcriptase inhibitorsthat may be administered in combination with the compositions of theinvention, include, but are not limited to, VIRAMUNE™ (nevirapine),RESCRIPTOR™ (delavirdine), and SUSTIVA™ (efavirenz). Protease inhibitorsthat may be administered in combination with the compositions of theinvention, include, but are not limited to, CRIXIVAN™ (indinavir),NORVIR™ (ritonavir), INVIRASE™ (saquinavir), and VIRACEPT™ (nelfinavir).In a specific embodiment, antiretroviral agents, nucleoside reversetranscriptase inhibitors, non-nucleoside reverse transcriptaseinhibitors, and/or protease inhibitors may be used in any combinationwith compositions of the invention to treat, prevent, and/or diagnoseAIDS and/or to treat, prevent, and/or diagnose HIV infection.

In other embodiments, compositions of the invention may be administeredin combination with anti-opportunistic infection agents.Anti-opportunistic agents that may be administered in combination withthe compositions of the invention, include, but are not limited to,TRIMETHOPRIM-SULFAMETHOXAZOLE™, DAPSONE™, PENTAMIDINE™, ATOVAQUONE™,ISONIAZID™, RIFAMPIN™, PYRAZINAMIDE™, ETHAMBUTOL™, RIFABUTIN™,CLARITHROMYCIN™, AZITHROMYCIN™, GANCICLOVIR™, FOSCARNET™, CIDOFOVIR™,FLUCONAZOLE™, ITRACONAZOLE™, KETOCONAZOLE™, ACYCLOVIR™, FAMCICOLVIR™,PYRIMETHAMINE™, LEUCOVORIN™, NEUPOGEN™ (filgrastim/G-CSF), and LEUKINE™(sargramostim/GM-CSF). In a specific embodiment, compositions of theinvention are used in any combination withTRIMETHOPRIM-SULFAMETHOXAZOLE™, DAPSONE™, PENTAMIDINE™, and/orATOVAQUONE™ to prophylactically treat, prevent, and/or diagnose anopportunistic Pneumocystis carinii pneumonia infection. In anotherspecific embodiment, compositions of the invention are used in anycombination with ISONIAZID™, RIFAMPIN™, PYRAZINAMIDE™, and/orETHAMBUTOL™ to prophylactically treat, prevent, and/or diagnose anopportunistic Mycobacterium avium complex infection. In another specificembodiment, compositions of the invention are used in any combinationwith RIFABUTIN™, CLARITHROMYCIN™, and/or AZITHROMYCIN™ toprophylactically treat, prevent, and/or diagnose an opportunisticMycobacterium tuberculosis infection. In another specific embodiment,compositions of the invention are used in any combination withGANCICLOVIR™, FOSCARNET™, and/or CIDOFOVIR™ to prophylactically treat,prevent, and/or diagnose an opportunistic cytomegalovirus infection. Inanother specific embodiment, compositions of the invention are used inany combination with FLUCONAZOLE™, ITRACONAZOLE™, and/or KETOCONAZOLE™to prophylactically treat, prevent, and/or diagnose an opportunisticfungal infection. In another specific embodiment, compositions of theinvention are used in any combination with ACYCLOVIR™ and/orFAMCICOLVIR™ to prophylactically treat, prevent, and/or diagnose anopportunistic herpes simplex virus type I and/or type II infection.

In another specific embodiment, compositions of the invention are usedin any combination with PYRIMETHAMINE™ and/or LEUCOVORIN™ toprophylactically treat, prevent, and/or diagnose an opportunisticToxoplasma gondii infection. In another specific embodiment,compositions of the invention are used in any combination withLEUCOVORIN™ and/or NEUPOGEN™ to prophylactically treat, prevent, and/ordiagnose an opportunistic bacterial infection.

In a further embodiment, the compositions of the invention areadministered in combination with an antiviral agent. Antiviral agentsthat may be administered with the compositions of the invention include,but are not limited to, acyclovir, ribavirin, amantadine, andremantidine.

In a further embodiment, the compositions of the invention areadministered in combination with an antibiotic agent. Antibiotic agentsthat may be administered with the compositions of the invention include,but are not limited to, amoxicillin, aminoglycosides, beta-lactam(glycopeptide), beta-lactamases, Clindamycin, chloramphenicol,cephalosporins, ciprofloxacin, ciprofloxacin, erythromycin,fluoroquinolones, macrolides, metronidazole, penicillins, quinolones,rifampin, streptomycin, sulfonamide, tetracyclines, trimethoprim,trimethoprim-sulfamthoxazole, and vancomycin.

Conventional nonspecific immunosuppressive agents, that may beadministered in combination with the compositions of the inventioninclude, but are not limited to, steroids, cyclosporine, cyclosporineanalogs cyclophosphamide, cyclophosphamide IV, methylprednisolone,prednisolone, azathioprine, FK-506, 15-deoxyspergualin, and otherimmunosuppressive agents that act by suppressing the function ofresponding T cells.

In specific embodiments, compositions of the invention are administeredin combination with immunosuppressants. Immunosuppressants preparationsthat may be administered with the compositions of the invention include,but are not limited to, ORTHOCLONE™ (OKT3), SANDIMMUNE™/NEORAL™/SANGDYA™(cyclosporin), PROGRAF™ (tacrolimus), CELLCEPT™ (mycophenolate),Azathioprine, glucorticosteroids, and RAPAMUNE™ (sirolimus). In aspecific embodiment, immunosuppressants may be used to prevent rejectionof organ or bone marrow transplantation.

In a preferred embodiment, the compositions of the invention areadministered in combination with steroid therapy. Steroids that may beadministered in combination with the compositions of the invention,include, but are not limited to, oral corticosteroids, prednisone, andmethylprednisolone (e.g., IV methylprednisolone). In a specificembodiment, compositions of the invention are administered incombination with prednisone. In a further specific embodiment, thecompositions of the invention are administered in combination withprednisone and an immunosuppressive agent. Immunosuppressive agents thatmay be administered with the compositions of the invention andprednisone are those described herein, and include, but are not limitedto, azathioprine, cylophosphamide, and cyclophosphamide IV. In a anotherspecific embodiment, compositions of the invention are administered incombination with methylprednisolone. In a further specific embodiment,the compositions of the invention are administered in combination withmethylprednisolone and an immunosuppressive agent. Immunosuppressiveagents that may be administered with the compositions of the inventionand methylprednisolone are those described herein, and include, but arenot limited to, azathioprine, cylophosphamide, and cyclophosphamide IV.

In a preferred embodiment, the compositions of the invention areadministered in combination with an antimalarial. Antimalarials that maybe administered with the compositions of the invention include, but arenot limited to, hydroxychloroquine, chloroquine, and/or quinacrine.

In a preferred embodiment, the compositions of the invention areadministered in combination with an NSAID.

In a nonexclusive embodiment, the compositions of the invention areadministered in combination with one, two, three, four, five, ten, ormore of the following drugs: NRD-101 (Hoechst Marion Roussel),diclofenac (Dimethaid), oxaprozin potassium (Monsanto), mecasermin(Chiron), T-614 (Toyama), pemetrexed disodium (Eli Lilly), atreleuton(Abbott), valdecoxib (Monsanto), eltenac (Byk Gulden), campath, AGM-1470(Takeda), CDP-571 (Celltech Chiroscience), CM-101 (CarboMed), ML-3000(Merckle), CB-2431 (KS Biomedix), CBF-BS2 (KS Biomedix), IL-1Ra genetherapy (Valentis), JTE-522 (Japan Tobacco), paclitaxel (Angiotech),DW-166HC (Dong Wha), darbufelone mesylate (Warner-Lambert), soluble TNFreceptor 1 (synergen; Amgen), IPR-6001 (Institute for PharmaceuticalResearch), trocade (Hoffman-La Roche), EF-5 (Scotia Pharmaceuticals),BIIL-284 (Boehringer Ingelheim), BIIF-1149 (Boehringer Ingelheim),LeukoVax (Inflammatics), MK-663 (Merck), ST-1482 (Sigma-Tau), andbutixocort propionate (WarnerLambert).

In a preferred embodiment, the compositions of the invention areadministered in combination with one, two, three, four, five or more ofthe following drugs: methotrexate, sulfasalazine, sodium aurothiomalate,auranofin, cyclosporine, penicillamine, azathioprine, an antimalarialdrug (e.g., as described herein), cyclophosphamide, chlorambucil, gold,ENBREL™ (Etanercept), anti-TNF antibody, and prednisolone.

In a more preferred embodiment, the compositions of the invention areadministered in combination with an antimalarial, methotrexate, anti-TNFantibody, ENBREL™ and/or suflasalazine. In one embodiment, thecompositions of the invention are administered in combination withmethotrexate. In another embodiment, the compositions of the inventionare administered in combination with anti-TNF antibody. In anotherembodiment, the compositions of the invention are administered incombination with methotrexate and anti-TNF antibody. In anotherembodiment, the compositions of the invention are administered incombination with suflasalazine. In another specific embodiment, thecompositions of the invention are administered in combination withmethotrexate, anti-TNF antibody, and suflasalazine. In anotherembodiment, the compositions of the invention are administered incombination ENBREL™. In another embodiment, the compositions of theinvention are administered in combination with ENBREL™ and methotrexate.In another embodiment, the compositions of the invention areadministered in combination with ENBREL™, methotrexate andsuflasalazine. In another embodiment, the compositions of the inventionare administered in combination with ENBREL™, methotrexate andsuflasalazine. In other embodiments, one or more antimalarials iscombined with one of the above-recited combinations. In a specificembodiment, the compositions of the invention are administered incombination with an antimalarial (e.g., hydroxychloroquine), ENBREL™,methotrexate and suflasalazine. In another specific embodiment, thecompositions of the invention are administered in combination with anantimalarial (e.g., hydroxychloroquine), sulfasalazine, anti-TNFantibody, and methotrexate.

In an additional embodiment, compositions of the invention areadministered alone or in combination with one or more intravenous immuneglobulin preparations. Intravenous immune globulin preparations that maybe administered with the compositions of the invention include, but notlimited to, GAMMAR™, IVEEGAM™, SANDOGLOBULIN™, GAMMAGARD S/D™, andGAMIMUNE™. In a specific embodiment, compositions of the invention areadministered in combination with intravenous immune globulinpreparations in transplantation therapy (e.g., bone marrow transplant).

CD40 ligand (CD40L), a soluble form of CD40L (e.g., AVREND™),biologically active fragments, variants, or derivatives of CD40L,anti-CD40L antibodies (e.g., agonistic or antagonistic antibodies),and/or anti-CD40 antibodies (e.g., agonistic or antagonisticantibodies).

In an additional embodiment, the compositions of the invention areadministered alone or in combination with an anti-inflammatory agent.Anti-inflammatory agents that may be administered with the compositionsof the invention include, but are not limited to, glucocorticoids andthe nonsteroidal anti-inflammatories, aminoarylcarboxylic acidderivatives, arylacetic acid derivatives, arylbutyric acid derivatives,arylcarboxylic acids, arylpropionic acid derivatives, pyrazoles,pyrazolones, salicylic acid derivatives, thiazinecarboxamides,e-acetamidocaproic acid, S-adenosylmethionine, 3-amino-4-hydroxybutyricacid, amixetrine, bendazac, benzydamine, bucolome, difenpiramide,ditazol, emorfazone, guaiazulene, nabumetone, nimesulide, orgotein,oxaceprol, paranyline, perisoxal, pifoxime, proquazone, proxazole, andtenidap.

In another embodiment, compositions of the invention are administered incombination with a chemotherapeutic agent. Chemotherapeutic agents thatmay be administered with the compositions of the invention include, butare not limited to, antibiotic derivatives (e.g., doxorubicin,bleomycin, daunorubicin, and dactinomycin); antiestrogens (e.g.,tamoxifen); antimetabolites (e.g., fluorouracil, 5-FU, methotrexate,floxuridine, interferon alpha-2b, glutamic acid, plicamycin,mercaptopurine, and 6-thioguanine); cytotoxic agents (e.g., carmustine,BCNU, lomustine, CCNU, cytosine arabinoside, cyclophosphamide,estramustine, hydroxyurea, procarbazine, mitomycin, busulfan,cis-platin, and vincristine sulfate); hormones (e.g.,medroxyprogesterone, estramustine phosphate sodium, ethinyl estradiol,estradiol, megestrol acetate, methyltestosterone, diethylstilbestroldiphosphate, chlorotrianisene, and testolactone); nitrogen mustardderivatives (e.g., mephalen, chorambucil, mechlorethamine (nitrogenmustard) and thiotepa); steroids and combinations (e.g., bethamethasonesodium phosphate); and others (e.g., dicarbazine, asparaginase,mitotane, vincristine sulfate, vinblastine sulfate, and etoposide).

In a specific embodiment, compositions of the invention are administeredin combination with CHOP (cyclophosphamide, doxorubicin, vincristine,and prednisone) or any combination of the components of CHOP. In anotherembodiment, compositions of the invention are administered incombination with Rituximab. In a further embodiment, compositions of theinvention are administered with Rituxmab and CHOP, or Rituxmab and anycombination of the components of CHOP.

In an additional embodiment, the compositions of the invention areadministered in combination with cytokines. Cytokines that may beadministered with the compositions of the invention include, but are notlimited to, GM-CSF, G-CSF, IL2, IL3, IL4, IL5, IL6, IL7, IL10, IL12,IL13, IL15, anti-CD40, CD40L, IFN-alpha, IFN-beta, IFN-gamma, TNF-alpha,and TNF-beta. In another embodiment, compositions of the invention maybe administered with any interleukin, including, but not limited to,IL-1 alpha, IL-1beta, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9,IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-19,IL-20, IL-21, and IL-22. In preferred embodiments, the compositions ofthe invention are administered in combination with IL4 and IL10. BothIL4 and IL10 have been observed by the inventors to enhanceNeutrokine-alpha mediated B cell proliferation.

In an additional embodiment, the compositions of the invention areadministered with a chemokine. In another embodiment, the compositionsof the invention are administered with chemokine beta-8, chemokinebeta-1, and/or macrophage inflammatory protein-4. In a preferredembodiment, the compositions of the invention are administered withchemokine beta-8.

In an additional embodiment, the compositions of the invention areadministered in combination with an IL-4 antagonist. IL-4 antagoniststhat may be administered with the compositions of the invention include,but are not limited to: soluble IL-4 receptor polypeptides, multimericforms of soluble IL-4 receptor polypeptides; anti-IL-4 receptorantibodies that bind the IL-4 receptor without transducing thebiological signal elicited by IL-4, anti-IL4 antibodies that blockbinding of IL-4 to one or more IL-4 receptors, and muteins of IL-4 thatbind IL-4 receptors but do not transduce the biological signal elicitedby IL-4. Preferably, the antibodies employed according to this methodare monoclonal antibodies (including antibody fragments, such as, forexample, those described herein).

In an additional embodiment, the compositions of the invention areadministered in combination with hematopoietic growth factors.Hematopoietic growth factors that may be administered with thecompositions of the invention include, but are not limited to, LEUKINE™(SARGRAMOSTIM™) and NEUPOGEN™ (FILGRASTIM™).

In an additional embodiment, the compositions of the invention areadministered in combination with fibroblast growth factors. Fibroblastgrowth factors that may be administered with the compositions of theinvention include, but are not limited to, FGF-1, FGF-2, FGF-3, FGF-4,FGF-5, FGF-6, FGF-7, FGF-8, FGF-9, FGF-10, FGF-11, FGF-12, FGF-13,FGF-14, and FGF-15.

Additionally, the compositions of the invention may be administeredalone or in combination with other therapeutic regimens, including butnot limited to, radiation therapy. Such combinatorial therapy may beadministered sequentially and/or concomitantly.

Agonists and Antagonists—Assays and Molecules

The invention also provides a method of screening compounds to identifythose which enhance or block the action of Neutrokine-alpha and/orNeutrokine-alphaSV polypeptide on cells, such as its interaction withNeutrokine-alpha and/or Neutrokine-alphaSV binding molecules such asreceptor molecules. An agonist is a compound which increases the naturalbiological functions of Neutrokine-alpha and/or Neutrokine-alphaSV orwhich functions in a manner similar to Neutrokine-alpha and/orNeutrokine-alphaSV while antagonists decrease or eliminate suchfunctions.

In another embodiment, the invention provides a method for identifying areceptor protein or other ligand-binding protein which bindsspecifically to a Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide. For example, a cellular compartment, such as a membrane ora preparation thereof, may be prepared from a cell that expresses amolecule that binds Neutrokine-alpha and/or Neutrokine-alphaSV. Thepreparation is incubated with labeled Neutrokine-alpha and/orNeutrokine-alphaSV and complexes of Neutrokine-alpha and/orNeutrokine-alphaSV bound to the receptor or other binding protein areisolated and characterized according to routine methods known in theart. Alternatively, the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide may be bound to a solid support so that binding moleculessolubilized from cells are bound to the column and then eluted andcharacterized according to routine methods.

In the assay of the invention for agonists or antagonists, a cellularcompartment, such as a membrane or a preparation thereof, may beprepared from a cell that expresses a molecule that bindsNeutrokine-alpha and/or Neutrokine-alphaSV such as a molecule of asignaling or regulatory pathway modulated by Neutrokine-alpha and/orNeutrokine-alphaSV. The preparation is incubated with labeledNeutrokine-alpha and/or Neutrokine-alphaSV in the absence or thepresence of a candidate molecule which may be a Neutrokine-alpha and/orNeutrokine-alphaSV agonist or antagonist. The ability of the candidatemolecule to bind the binding molecule is reflected in decreased bindingof the labeled ligand. Molecules which bind gratuitously, i.e., withoutinducing the effects of Neutrokine-alpha on binding the Neutrokine-alphaand/or Neutrokine-alphaSV binding molecule, are most likely to be goodantagonists. Molecules that bind well and elicit effects that are thesame as or closely related to Neutrokine-alpha and/or Neutrokine-alphaSVare agonists.

Neutrokine-alpha- and/or Neutrokine-alphaSV-like effects of potentialagonists and antagonists may by measured, for instance, by determiningactivity of a second messenger system following interaction of thecandidate molecule with a cell or appropriate cell preparation, andcomparing the effect with that of Neutrokine-alpha and/orNeutrokine-alphaSV or molecules that elicit the same effects asNeutrokine-alpha and/or Neutrokine-alphaSV. Second messenger systemsthat may be useful in this regard include but are not limited to AMPguanylate cyclase, ion channel or phosphoinositide hydrolysis secondmessenger systems.

Another example of an assay for Neutrokine-alpha and/orNeutrokine-alphaSV antagonists is a competitive assay that combinesNeutrokine-alpha and/or Neutrokine-alphaSV and a potential antagonistwith membrane-bound receptor molecules or recombinant Neutrokine-alphaand/or Neutrokine-alphaSV receptor molecules under appropriateconditions for a competitive inhibition assay. Neutrokine-alpha and/orNeutrokine-alphaSV can be labeled, such as by radioactivity, such thatthe number of Neutrokine-alpha and/or Neutrokine-alphaSV molecules boundto a receptor molecule can be determined accurately to assess theeffectiveness of the potential antagonist.

Potential antagonists include small organic molecules, peptides,polypeptides (e.g., IL-13), and antibodies that bind to a polypeptide ofthe invention and thereby inhibit or extinguish its activity. Potentialantagonists also may be small organic molecules, a peptide, apolypeptide such as a closely related protein or antibody that binds thesame sites on a binding molecule, such as a receptor molecule, withoutinducing Neutrokine-alpha and/or Neutrokine-alphaSV induced activities,thereby preventing the action of Neutrokine-alpha and/orNeutrokine-alphaSV by excluding Neutrokine-alpha and/orNeutrokine-alphaSV from binding.

Other potential antagonists include antisense molecules. Antisensetechnology can be used to control gene expression through antisense DNAor RNA or through triple-helix formation. Antisense techniques arediscussed, for example, in Okano, J. Neurochem. 56: 560 (1991);“Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRCPress, Boca Raton, Fla. (1988). Antisense technology can be used tocontrol gene expression through antisense DNA or RNA, or throughtriple-helix formation. Antisense techniques are discussed for example,in Okano, J., Neurochem. 56:560 (1991); Oligodeoxynucleotides asAntisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla.(1988). Triple helix formation is discussed in, for instance Lee et al.,Nucleic Acids Research 6: 3073 (1979); Cooney et al., Science 241: 456(1988); and Dervan et al., Science 251: 1360 (1991). The methods arebased on binding of a polynucleotide to a complementary DNA or RNA. Forexample, the 5′ coding portion of a polynucleotide that encodes theextracellular domain of the polypeptide of the present invention may beused to design an antisense RNA oligonucleotide of from about 10 to 40base pairs in length. A DNA oligonucleotide is designed to becomplementary to a region of the gene involved in transcription therebypreventing transcription and the production of Neutrokine-alpha and/orNeutrokine-alphaSV. The antisense RNA oligonucleotide hybridizes to themRNA in vivo and blocks translation of the mRNA molecule intoNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide. Theoligonucleotides described above can also be delivered to cells suchthat the antisense RNA or DNA may be expressed in vivo to inhibitproduction of Neutrokine-alpha and/or Neutrokine-alphaSV.

In one embodiment, the Neutrokine-alpha and/or Neutrokine-alphaSVantisense nucleic acid of the invention is produced intracellularly bytranscription from an exogenous sequence. For example, a vector or aportion thereof, is transcribed, producing an antisense nucleic acid(RNA) of the invention. Such a vector would contain a sequence encodingthe Neutrokine-alpha and/or Neutrokine-alphaSV antisense nucleic acid.Such a vector can remain episomal or become chromosomally integrated, aslong as it can be transcribed to produce the desired antisense RNA. Suchvectors can be constructed by recombinant DNA technology methodsstandard in the art. Vectors can be plasmid, viral, or others known inthe art, used for replication and expression in vertebrate cells.Expression of the sequence encoding Neutrokine-alpha and/orNeutrokine-alphaSV, or fragments thereof, can be by any promoter knownin the art to act in vertebrate, preferably human cells. Such promoterscan be inducible or constitutive. Such promoters include, but are notlimited to, the SV40 early promoter region (Bernoist and Chambon, Nature29:304-310 (1981), the promoter contained in the 3′ long terminal repeatof Rous sarcoma virus (Yamamoto et al., Cell 22:787-797 (1980), theherpes thymidine promoter (Wagner et al., Proc. Natl. Acad. Sci. U.S.A.78:1441-1445 (1981), the regulatory sequences of the metallothioneingene (Brinster, et al., Nature 296:39-42 (1982)), etc.

The antisense nucleic acids of the invention comprise a sequencecomplementary to at least a portion of an RNA transcript of aNeutrokine-alpha and/or Neutrokine-alphaSV gene. However, absolutecomplementarity, although preferred, is not required. A sequence“complementary to at least a portion of an RNA,” referred to herein,means a sequence having sufficient complementarity to be able tohybridize with the RNA, forming a stable duplex; in the case of doublestranded Neutrokine-alpha and/or Neutrokine-alphaSV antisense nucleicacids, a single strand of the duplex DNA may thus be tested, or triplexformation may be assayed. The ability to hybridize will depend on boththe degree of complementarity and the length of the antisense nucleicacid Generally, the larger the hybridizing nucleic acid, the more basemismatches with a Neutrokine-alpha and/or Neutrokine-alphaSV RNA it maycontain and still form a stable duplex (or triplex as the case may be).One skilled in the art can ascertain a tolerable degree of mismatch byuse of standard procedures to determine the melting point of thehybridized complex.

Oligonucleotides that are complementary to the 5′ end of the message,e.g., the 5′ untranslated sequence up to and including the AUGinitiation codon, should work most efficiently at inhibitingtranslation. However, sequences complementary to the 3′ untranslatedsequences of mRNAs have been shown to be effective at inhibitingtranslation of mRNAs as well. See generally, Wagner, R., 1994, Nature372:333-335. Thus, oligonucleotides complementary to either the 5′- or3′-non-translated, non-coding regions of Neutrokine-alpha andNeutrokine-alphaSV shown in FIGS. 1A-B and 5A-B, respectively, could beused in an antisense approach to inhibit translation of endogenousNeutrokine-alpha and/or Neutrokine-alphaSV mRNA. Oligonucleotidescomplementary to the 5′ untranslated region of the mRNA should includethe complement of the AUG start codon. Antisense oligonucleotidescomplementary to mRNA coding regions are less efficient inhibitors oftranslation but could be used in accordance with the invention. Whetherdesigned to hybridize to the 5′-, 3′- or coding region ofNeutrokine-alpha and/or Neutrokine-alphaSV mRNA, antisense nucleic acidsshould be at least six nucleotides in length, and are preferablyoligonucleotides ranging from 6 to about 50 nucleotides in length. Inspecific aspects the oligonucleotide is at least 10 nucleotides, atleast 17 nucleotides, at least 25 nucleotides or at least 50nucleotides.

The polynucleotides of the invention can be DNA or RNA or chimericmixtures or derivatives or modified versions thereof, single-stranded ordouble-stranded. The oligonucleotide can be modified at the base moiety,sugar moiety, or phosphate backbone, for example, to improve stabilityof the molecule, hybridization, etc. The oligonucleotide may includeother appended groups such as peptides (e.g., for targeting host cellreceptors in vivo), or agents facilitating transport across the cellmembrane (see, e.g., Letsinger et al., 1989, Proc. Natl. Acad. Sci.U.S.A. 86:6553-6556; Lemaitre et al., Proc. Natl. Acad. Sci. 84:648-652(1987); PCT Publication No. WO88/09810, published Dec. 15, 1988) or theblood-brain barrier (see, e.g., PCT Publication No. WO89/10134,published Apr. 25, 1988), hybridization-triggered cleavage agents. (See,e.g., Krol et al., BioTechniques 6:958-976 (1988)) or intercalatingagents. (See, e.g., Zon, Pharm. Res. 5:539-549 (1988)). To this end, theoligonucleotide may be conjugated to another molecule, e.g., a peptide,hybridization triggered cross-linking agent, transport agent,hybridization-triggered cleavage agent, etc.

The antisense oligonucleotide may comprise at least one modified basemoiety which is selected from the group including, but not limited to,5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil,hypoxanthine, xantine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,5-methoxycarboxymethyluracil, 5-methoxyuracil,2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v),wybutoxosine, pseudouracil, queosine, 2-thiocytosine,5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v),5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w,and 2,6-diaminopurine.

The antisense oligonucleotide may also comprise at least one modifiedsugar moiety selected from the group including, but not limited to,arabinose, 2-fluoroarabinose, xylulose, and hexose.

In yet another embodiment, the antisense oligonucleotide comprises atleast one modified phosphate backbone selected from the group including,but not limited to, a phosphorothioate, a phosphorodithioate, aphosphoramidothioate, a phosphoramidate, a phosphordiamidate, amethylphosphonate, an alkyl phosphotriester, and a formacetal or analogthereof.

In yet another embodiment, the antisense oligonucleotide is analpha-anomeric oligonucleotide. An alpha-anomeric oligonucleotide formsspecific double-stranded hybrids with complementary RNA in which,contrary to the usual beta-units, the strands run parallel to each other(Gautier et al., Nucl. Acids Res. 15:6625-6641 (1987)). Theoligonucleotide is a 2-0-methylribonucleotide (Inoue et al., Nucl. AcidsRes. 15:6131-6148 (1987)), or a chimeric RNA-DNA analogue (Inoue et al.,FEBS Lett. 215:327-330 (1997)).

Polynucleotides of the invention may be synthesized by standard methodsknown in the art, e.g., by use of an automated DNA synthesizer (such asare commercially available from Biosearch, Applied Biosystems, etc.). Asexamples, phosphorothioate oligonucleotides may be synthesized by themethod of Stein et al. (Nucl. Acids Res. 16:3209 (1988)),methylphosphonate oligonucleotides can be prepared by use of controlledpore glass polymer supports (Sarin et al., Proc. Natl. Acad. Sci. U.S.A.85:7448-7451 (1988)), etc.

While antisense nucleotides complementary to the Neutrokine-alpha and/orNeutrokine-alphaSV coding region sequence could be used, thosecomplementary to the transcribed untranslated region are most preferred.

Potential antagonists according to the invention also include catalyticRNA, or a ribozyme (See, e.g., PCT International Publication WO90/11364, published Oct. 4, 1990; Sarver et al, Science 247:1222-1225(1990). While ribozymes that cleave mRNA at site specific recognitionsequences can be used to destroy Neutrokine-alpha and/orNeutrokine-alphaSV mRNAs, the use of hammerhead ribozymes is preferred.Hammerhead ribozymes cleave mRNAs at locations dictated by flankingregions that form complementary base pairs with the target mRNA. Thesole requirement is that the target mRNA have the following sequence oftwo bases: 5′-UG-3′. The construction and production of hammerheadribozymes is well known in the art and is described more fully inHaseloff and Gerlach, Nature 334:585-591 (1988). There are numerouspotential hammerhead ribozyme cleavage sites within the nucleotidesequence of Neutrokine-alpha and Neutrokine-alphaSV (FIGS. 1A-B and5A-B, respectively). Preferably, the ribozyme is engineered so that thecleavage recognition site is located near the 5′ end of theNeutrokine-alpha and/or Neutrokine-alphaSV mRNA; i.e., to increaseefficiency and minimize the intracellular accumulation of non-functionalmRNA transcripts.

As in the antisense approach, the ribozymes of the invention can becomposed of modified oligonucleotides (e.g., for improved stability,targeting, etc.) and should be delivered to cells which expressNeutrokine-alpha and/or Neutrokine-alphaSV in vivo. DNA constructsencoding the ribozyme may be introduced into the cell in the same manneras described above for the introduction of antisense encoding DNA. Apreferred method of delivery involves using a DNA construct “encoding”the ribozyme under the control of a strong constitutive promoter, suchas, for example, pol III or pol II promoter, so that transfected cellswill produce sufficient quantities of the ribozyme to destroy endogenousNeutrokine-alpha and/or Neutrokine-alphaSV messages and inhibittranslation. Since ribozymes unlike antisense molecules, are catalytic,a lower intracellular concentration is required for efficiency.

Endogenous gene expression can also be reduced by inactivating or“knocking out” the Neutrokine-alpha and/or Neutrokine-alphaSV geneand/or its promoter using targeted homologous recombination. (E.g., seeSmithies et al., Nature 317:230-234 (1985); Thomas & Capecchi, Cell51:503-512 (1987); Thompson et al., Cell 5:313-321 (1989); each of whichis incorporated by reference herein in its entirety). For example, amutant, non-functional polynucleotide of the invention (or a completelyunrelated DNA sequence) flanked by DNA homologous to the endogenouspolynucleotide sequence (either the coding regions or regulatory regionsof the gene) can be used, with or without a selectable marker and/or anegative selectable marker, to transfect cells that express polypeptidesof the invention in vivo. In another embodiment, techniques known in theart are used to generate knockouts in cells that contain, but do notexpress the gene of interest. Insertion of the DNA construct, viatargeted homologous recombination, results in inactivation of thetargeted gene. Such approaches are particularly suited in research andagricultural fields where modifications to embryonic stem cells can beused to generate animal offspring with an inactive targeted gene (e.g.,see Thomas & Capecchi 1987 and Thompson 1989, supra). However thisapproach can be routinely adapted for use in humans provided therecombinant DNA constructs are directly administered or targeted to therequired site in vivo using appropriate viral vectors that will beapparent to those of skill in the art. The contents of each of thedocuments recited in this paragraph is herein incorporated by referencein its entirety.

In other embodiments, antagonists according to the present inventioninclude soluble forms of Neutrokine-alpha and/or Neutrokine-alphaSV(e.g., fragments of Neutrokine-alpha shown in FIGS. 1A-B that includethe ligand binding domain, TNF conserved domain, and/or extracellulardomain of Neutrokine-alpha and/or Neutrokine-alphaSV and fragments ofNeutrokine-alphaSV shown in FIGS. 5A-B that include the ligand bindingdomain, TNF conserved domain, and/or extracellular domain ofNeutrokine-alpha and/or Neutrokine-alphaSV). Such soluble forms of theNeutrokine-alpha and/or Neutrokine-alphaSV, which may be naturallyoccurring or synthetic, antagonize Neutrokine-alpha and/orNeutrokine-alphaSV mediated signaling by competing with nativeNeutrokine-alpha and/or Neutrokine-alphaSV for binding toNeutrokine-alpha and/or Neutrokine-alphaSV receptors (e.g., DR5 (See,International Publication No. WO 98/41629), TR10 (See, InternationalPublication No. WO 98/54202), 312C2 (See, International Publication No.WO 98/06842), and TR11, TR11SV1, and TR11SV2 (See, U.S. application Ser.No. 09/176,200, now U.S. Pat. No. 6,509,173)), and/or by forming amultimer that may or may not be capable of binding the receptor, butwhich is incapable of inducing signal transduction. Preferably, theseantagonists inhibit Neutrokine-alpha and/or Neutrokine-alphaSV mediatedstimulation of lymphocyte (e.g., B-cell) proliferation, differentiation,and/or activation. Antagonists of the present invention also includeantibodies specific for TNF-family ligands (e.g., CD30) andNeutrokine-alpha-Fc and/or Neutrokine-alphaSV-Fc fusion proteins.

By a “TNF-family ligand” is intended naturally occurring, recombinant,and synthetic ligands that are capable of binding to a member of the TNFreceptor family and inducing and/or blocking the ligand/receptorsignaling pathway. Members of the TNF ligand family include, but are notlimited to, TNF-alpha, lymphotoxin-alpha (LT-alpha, also known asTNF-beta), LT-beta (found in complex heterotrimer LT-alpha2-beta), FasL,CD40L, (TNF-gamma (International Publication No. WO 96/14328), AIM-I(International Publication No. WO 97/33899), AIM-II (InternationalPublication No. WO 97/34911), APRIL (J. Exp. Med. 188(6):1185-1190),endokine-alpha (International Publication No. WO 98/07880),neutrokine-alpha (International Publication No. WO 98/18921), CD27L,CD30L, 4-1BBL, OX40L, CD27, CD30, 4-1BB, OX40, and nerve growth factor(NGF). In preferred embodiments, the Neutrokine-alpha and/orNeutrokine-alphaSV TNF-family ligands of the invention are DR5 (See,International Publication No. WO 98/41629), TR10 (See, InternationalPublication No. WO 98/54202), 312C2 (See, International Publication No.WO 98/06842), and TR11, TR11SV1, and TR11SV2 (See, U.S. application Ser.No. 09/176,200, now U.S. Pat. No. 6,509,173).

Antagonists of the present invention also include antibodies specificfor TNF-family receptors or the Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention. Antibodies accordingto the present invention may be prepared by any of a variety of standardmethods using Neutrokine-alpha and/or Neutrokine-alphaSV immunogens ofthe present invention. As indicated, such Neutrokine-alpha and/orNeutrokine-alphaSV immunogens include the complete Neutrokine-alpha andNeutrokine-alphaSV polypeptides depicted in FIGS. 1A-B (SEQ ID NO:2) andFIGS. 5A-B (SEQ ID NO:19), respectively, (which may or may not includethe leader sequence) and Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide fragments comprising, for example, the ligand bindingdomain, TNF-conserved domain, extracellular domain, transmembranedomain, and/or intracellular domain, or any combination thereof.

Polyclonal and monoclonal antibody agonists or antagonists according tothe present invention can be raised according to the methods disclosedin Tartaglia and Goeddel, J. Biol. Chem. 267(7):4304-4307 (1992));Tartaglia et al., Cell 73:213-216 (1993)), and PCT Application WO94/09137 and are preferably specific to (i.e., bind uniquely topolypeptides of the invention having the amino acid sequence of SEQ IDNO:2. The term “antibody” (Ab) or “monoclonal antibody” (mAb) as usedherein is meant to include intact molecules as well as fragments thereof(such as, for example, Fab and F(ab′) fragments) which are capable ofbinding an antigen. Fab, Fab′ and F(ab′) fragments lack the Fc fragmentintact antibody, clear more rapidly from the circulation, and may haveless non-specific tissue binding of an intact antibody (Wahl et al., J.Nucl. Med., 24:316-325 (1983)).

In a preferred method, antibodies according to the present invention aremAbs. Such mAbs can be prepared using hybridoma technology (Kohler andMillstein, Nature 256:495-497 (1975) and U.S. Pat. No. 4,376,110; Harlowet al., Antibodies: A Laboratory Manual, Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 1988; Monoclonal Antibodies andHybridomas: A New Dimension in Biological Analyses, Plenum Press, NewYork, N.Y., 1980; Campbell, “Monoclonal Antibody Technology,” In:Laboratory Techniques in Biochemistry and Molecular Biology, Volume 13(Burdon et al., eds.), Elsevier, Amsterdam (1984)).

Proteins and other compounds which bind the Neutrokine-alpha and/orNeutrokine-alphaSV domains are also candidate agonists and antagonistsaccording to the present invention. Such binding compounds can be“captured” using the yeast two-hybrid system (Fields and Song, Nature340:245-246 (1989)). A modified version of the yeast two-hybrid systemhas been described by Roger Brent and his colleagues (Gyuris, Cell75:791-803 (1993); Zervos et al., Cell 72:223-232 (1993)). Preferably,the yeast two-hybrid system is used according to the present inventionto capture compounds which bind to the ligand binding domain,extracellular, intracellular, transmembrane, and death domain of theNeutrokine-alpha and/or Neutrokine-alphaSV. Such compounds are goodcandidate agonists and antagonists of the present invention.

For example, using the two-hybrid assay described above, theextracellular or intracellular domain of the Neutrokine-alpha and/orNeutrokine-alphaSV receptor, or a portion thereof, may be used toidentify cellular proteins which interact with Neutrokine-alpha and/orNeutrokine-alphaSV the receptor in vivo. Such an assay may also be usedto identify ligands with potential agonistic or antagonistic activity ofNeutrokine-alpha and/or Neutrokine-alphaSV receptor function. Thisscreening assay has previously been used to identify proteins whichinteract with the cytoplasmic domain of the murine TNF-R11 and led tothe identification of two receptor associated proteins. Rothe et al.,Cell 78:681 (1994). Such proteins and amino acid sequences which bind tothe cytoplasmic domain of the Neutrokine-alpha and/or Neutrokine-alphaSVreceptors are good candidate agonist and antagonist of the presentinvention.

Other screening techniques include the use of cells which express thepolypeptide of the present invention (for example, transfected CHOcells) in a system which measures extracellular pH changes caused byreceptor activation, for example, as described in Science, 246:181-296(1989). In another example, potential agonists or antagonists may becontacted with a cell which expresses the polypeptide of the presentinvention and a second messenger response, e.g., signal transduction maybe measured to determine whether the potential antagonist or agonist iseffective.

Agonists according to the present invention include naturally occurringand synthetic compounds such as, for example, TNF family ligand peptidefragments, transforming growth factor, neurotransmitters (such asglutamate, dopamine, N-methyl-D-aspartate), tumor suppressors (p53),cytolytic T cells and antimetabolites. Preferred agonists includechemotherapeutic drugs such as, for example, cisplatin, doxorubicin,bleomycin, cytosine arabinoside, nitrogen mustard, methotrexate andvincristine. Others include ethanol and -amyloid peptide. (Science267:1457-1458 (1995)).

Preferred agonists are fragments of Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides of the invention which stimulatelymphocyte (e.g., B cell) proliferation, differentiation and/oractivation. Further preferred agonists include polyclonal and monoclonalantibodies raised against the Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptides of the invention, or a fragment thereof. Such agonistantibodies raised against a TNF-family receptor are disclosed inTartaglia et al., Proc. Natl. Acad. Sci. USA 88:9292-9296 (1991); andTartaglia et al., J. Biol. Chem. 267:4304-4307 (1992). See, also, PCTApplication WO 94/09137.

In an additional embodiment, immunoregulatory molecules such as, forexample, IL2, IL3, IL4, IL5, IL6, IL7, IL10, IL12, IL13, IL15,anti-CD40, CD40L, IFN-gamma and TNF-alpha, may be used as agonists ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptides of the inventionwhich stimulate lymphocyte (e.g., B cell) proliferation, differentiationand/or activation. In a specific embodiment, IL4 and/or IL10 are used toenhance the Neutrokine-alpha- and/or Neutrokine-alphaSV-mediatedproliferation of B cells.

In further embodiments of the invention, cells that are geneticallyengineered to express the polypeptides of the invention, oralternatively, that are genetically engineered not to express thepolypeptides of the invention (e.g., knockouts) are administered to apatient in vivo. Such cells may be obtained from the patient (i.e.,animal, including human) or an MHC compatible donor and can include, butare not limited to fibroblasts, bone marrow cells, blood cells (e.g.,lymphocytes), adipocytes, muscle cells, endothelial cells etc. The cellsare genetically engineered in vitro using recombinant DNA techniques tointroduce the coding sequence of polypeptides of the invention into thecells, or alternatively, to disrupt the coding sequence and/orendogenous regulatory sequence associated with the polypeptides of theinvention, e.g., by transduction (using viral vectors, and preferablyvectors that integrate the transgene into the cell genome) ortransfection procedures, including, but not limited to, the use ofplasmids, cosmids, YACs, naked DNA, electroporation, liposomes, etc. Thecoding sequence of the polypeptides of the invention can be placed underthe control of a strong constitutive or inducible promoter orpromoter/enhancer to achieve expression, and preferably secretion, ofthe polypeptides of the invention. The engineered cells which expressand preferably secrete the polypeptides of the invention can beintroduced into the patient systemically, e.g., in the circulation, orintraperitoneally.

Alternatively, the cells can be incorporated into a matrix and implantedin the body, e.g., genetically engineered fibroblasts can be implantedas part of a skin graft; genetically engineered endothelial cells can beimplanted as part of a lymphatic or vascular graft. (See, for example,Anderson et al. U.S. Pat. No. 5,399,349; and Mulligan & Wilson, U.S.Pat. No. 5,460,959 each of which is incorporated by reference herein inits entirety).

When the cells to be administered are non-autologous or non-MHCcompatible cells, they can be administered using well known techniqueswhich prevent the development of a host immune response against theintroduced cells. For example, the cells may be introduced in anencapsulated form which, while allowing for an exchange of componentswith the immediate extracellular environment, does not allow theintroduced cells to be recognized by the host immune system.

In yet another embodiment of the invention, the activity ofNeutrokine-alpha and/or Neutrokine-alphaSV polypeptide can be reducedusing a “dominant negative.” To this end, constructs which encodedefective Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide, suchas, for example, mutants lacking all or a portion of the TNF-conserveddomain, can be used in gene therapy approaches to diminish the activityof Neutrokine-alpha and/or Neutrokine-alphaSV on appropriate targetcells. For example, nucleotide sequences that direct host cellexpression of Neutrokine-alpha and/or Neutrokine-alphaSV polypeptide inwhich all or a portion of the TNF-conserved domain is altered or missingcan be introduced into monocytic cells or other cells or tissues (eitherby in vivo or ex vivo gene therapy methods described herein or otherwiseknown in the art). Alternatively, targeted homologous recombination canbe utilized to introduce such deletions or mutations into the subject'sendogenous Neutrokine-alpha and/or Neutrokine-alphaSV gene in monocytes.The engineered cells will express non-functional Neutrokine-alpha and/orNeutrokine-alphaSV polypeptides (i.e., a ligand (e.g., multimer) thatmay be capable of binding, but which is incapable of inducing signaltransduction).

Chromosome Assays

The nucleic acid molecules of the present invention are also valuablefor chromosome identification. The sequence is specifically targeted toand can hybridize with a particular location on an individual humanchromosome. Moreover, there is a current need for identifying particularsites on the chromosome. Few chromosome marking reagents based on actualsequence data (repeat polymorphisms) are presently available for markingchromosomal location. The mapping of DNAs to chromosomes according tothe present invention is an important first step in correlating thosesequences with genes associated with disease.

In certain preferred embodiments in this regard, the cDNA and/orpolynucleotides herein disclosed is used to clone genomic DNA of aNeutrokine-alpha and/or Neutrokine-alphaSV gene. This can beaccomplished using a variety of well known techniques and libraries,which generally are available commercially. The genomic DNA then is usedfor in situ chromosome mapping using well known techniques for thispurpose.

In addition, in some cases, sequences can be mapped to chromosomes bypreparing PCR primers (preferably 15-25 bp) from the cDNA. Computeranalysis of the 3′ untranslated region of the gene is used to rapidlyselect primers that do not span more than one exon in the genomic DNA,thus complicating the amplification process. These primers are then usedfor PCR screening of somatic cell hybrids containing individual humanchromosomes. Fluorescence in situ hybridization (“FISH”) of a cDNA cloneto a metaphase chromosomal spread can be used to provide a precisechromosomal location in one step. This technique can be used with probesfrom the cDNA as short as 50 or 60 bp. For a review of this technique,see Verma et al., Human Chromosomes: A Manual Of Basic Techniques,Pergamon Press, New York (1988).

Once a sequence has been mapped to a precise chromosomal location, thephysical position of the sequence on the chromosome can be correlatedwith genetic map data. Such data are found, for example, in V. McKusick,Mendelian Inheritance In Man, available on-line through Johns HopkinsUniversity, Welch Medical Library. The relationship between genes anddiseases that have been mapped to the same chromosomal region are thenidentified through linkage analysis (coinheritance of physicallyadjacent genes).

Next, it is necessary to determine the differences in the cDNA orgenomic sequence between affected and unaffected individuals. If amutation is observed in some or all of the affected individuals but notin any normal individuals, then the mutation is likely to be thecausative agent of the disease.

With current resolution of physical mapping and genetic mappingtechniques, a cDNA precisely localized to a chromosomal regionassociated with the disease could be one of between 50 and 500 potentialcausative genes. (This assumes 1 megabase mapping resolution and onegene per 20 kb).

Utilizing the techniques described above, the chromosomal location ofNeutrokine-alpha and Neutrokine-alphaSV was determined with highconfidence using a combination of somatic cell hybrids and radiationhybrids to chromosome position 13q34.

EXAMPLES

Having generally described the invention, the same will be more readilyunderstood by reference to the following examples, which are provided byway of illustration and are not intended as limiting. Many of thefollowing examples are set forth referring specifically toNeutrokine-alpha polynucleotides and polypeptides of the invention. Eachexample may also be practiced to generate and/or examineNeutrokine-alphaSV polynucleotides and/or polypeptides of the invention.One of ordinary skill in the art would easily be able to direct thefollowing examples to Neutrokine-alphaSV.

Example 1a Expression and Purification of “His-Tagged” Neutrokine-Alphain E. coli

The bacterial expression vector pQE9 (pD10) is used for bacterialexpression in this example. (QIAGEN, Inc., supra). pQE9 encodesampicillin antibiotic resistance (“Ampr”) and contains a bacterialorigin of replication (“ori”), an IPTG inducible promoter, a ribosomebinding site (“RBS”), six codons encoding histidine residues that allowaffinity purification using nickel-nitrilo-tri-acetic acid (“Ni-NTA”)affinity resin sold by QIAGEN, Inc., supra, and suitable singlerestriction enzyme cleavage sites. These elements are arranged such thatan inserted DNA fragment encoding a polypeptide expresses thatpolypeptide with the six His residues (i.e., a “6×His tag”) covalentlylinked to the amino terminus of that polypeptide.

The DNA sequence encoding the desired portion of the Neutrokine-alphaprotein comprising the extracellular domain sequence is amplified fromthe deposited cDNA clone using PCR oligonucleotide primers which annealto the amino terminal sequences of the desired portion of the proteinand to sequences in the deposited construct 3′ to the cDNA codingsequence. Additional nucleotides containing restriction sites tofacilitate cloning in the pQE9 vector are added to the 5′ and 3′ primersequences, respectively.

For cloning the extracellular domain of the protein, the 5′ primer hasthe sequence 5′-GTG GGA TCC AGC CTC CGG GCA GAG CTG-3′ (SEQ ID NO:10)containing the underlined Bam HI restriction site followed by 18nucleotides of the amino terminal coding sequence of the extracellulardomain of the sequence in FIGS. 1A and 1B. One of ordinary skill in theart would appreciate, of course, that the point in the protein codingsequence where the 5′ primer begins may be varied to amplify a DNAsegment encoding any desired portion of the complete Neutrokine aprotein shorter or longer than the extracellular domain of the form. The3′ primer has the sequence 5′-GTG AAG CTT TTA TTA CAG CAG TTT CAA TGCACC-3′ (SEQ ID NO:11) containing the underlined Hind III restrictionsite followed by two stop codons and 18 nucleotides complementary to the3′ end of the coding sequence of the DNA sequence in FIGS. 1A and 1B.

The amplified DNA fragment and the vector pQE9 are digested with Bam HIand Hind III and the digested DNAs are then ligated together. Insertionof the DNA into the restricted pQE9 vector places the protein codingregion downstream from the IPTG-inducible promoter and in-frame with aninitiating AUG and the six histidine codons.

The ligation mixture is transformed into competent E. coli cells usingstandard procedures such as those described in Sambrook et al.,Molecular Cloning: a Laboratory Manual, 2nd Ed.; Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (1989). E. coli strainM15/rep4, containing multiple copies of the plasmid pREP4, whichexpresses the lac repressor and confers kanamycin resistance(“Kan^(r)”), is used in carrying out the illustrative example describedherein. This strain, which is only one of many that are suitable forexpressing protein, is available commercially from QIAGEN, Inc., supra.Transformants are identified by their ability to grow on LB plates inthe presence of ampicillin and kanamycin. Plasmid DNA is isolated fromresistant colonies and the identity of the cloned DNA confirmed byrestriction analysis, PCR and DNA sequencing. Clones containing thedesired constructs are grown overnight (“O/N”) in liquid culture in LBmedia supplemented with both ampicillin (100 μg/ml) and kanamycin (25μg/ml). The O/N culture is used to inoculate a large culture, at adilution of approximately 1:25 to 1:250. The cells are grown to anoptical density at 600 nm (“OD600”) of between 0.4 and 0.6.Isopropyl-beta-D-thiogalactopyranoside (“IPTG”) is then added to a finalconcentration of 1 mM to induce transcription from the lac repressorsensitive promoter, by inactivating the lad repressor. Cellssubsequently are incubated further for 3 to 4 hours. Cells then areharvested by centrifugation.

The cells are then stirred for 3-4 hours at 4° C. in 6M guanidine-HCl,pH 8. The cell debris is removed by centrifugation, and the supernatantcontaining the is loaded on to a nickel-nitrilo-tri-acetic acid(“Ni-NTA”) affinity resin column (available from QIAGEN, Inc., supra).Proteins with a 6×His tag bind to the Ni-NTA resin with high affinityand can be purified in a simple one-step procedure (for details see: TheQIAexpressionist, 1995, QIAGEN, Inc., supra). Briefly the supernatant isloaded on to the column in 6 M guanidine-HCl, pH 8, the column is firstwashed with 10 volumes of 6 M guanidine-HCl, pH 8, then washed with 10volumes of 6 M guanidine-HCl pH 6, and finally the Neutrokine-alphaand/or Neutrokine-alphaSV polypeptide is eluted with 6 M guanidine-HCl,pH 5.

The purified protein is then renatured by dialyzing it againstphosphate-buffered saline (PBS) or 50 mM Na-acetate, pH 6 buffer plus200 mM NaCl. Alternatively, the protein can be successfully refoldedwhile immobilized on the Ni-NTA column. The recommended conditions areas follows: renature using a linear 6M-1M urea gradient in 500 mM NaCl,20% glycerol, 20 mM Tris/HCl pH 7.4, containing protease inhibitors. Therenaturation should be performed over a period of 1.5 hours or more.After renaturation the proteins can be eluted by the addition of 250 mMimmidazole. Immidazole is removed by a final dialyzing step against PBSor 50 mM sodium acetate pH 6 buffer plus 200 mM NaCl. The purifiedprotein is stored at 4° C. or frozen at −80° C.

Example 1b Expression and Purification of Neutrokine-Alpha in E. coli

The bacterial expression vector pQE60 is used for bacterial expressionin this example. (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif.,91311). pQE60 encodes ampicillin antibiotic resistance (“Ampr”) andcontains a bacterial origin of replication (“ori”), an IPTG induciblepromoter, a ribosome binding site (“RBS”), six codons encoding histidineresidues that allow affinity purification usingnickel-nitrilo-tri-acetic acid (“Ni-NTA”) affinity resin sold by QIAGEN,Inc., supra, and suitable single restriction enzyme cleavage sites.These elements are arranged such that a DNA fragment encoding apolypeptide may be inserted in such as way as to produce thatpolypeptide with the six His residues (i.e., a “6×His tag”) covalentlylinked to the carboxyl terminus of that polypeptide. However, in thisexample, the polypeptide coding sequence is inserted such thattranslation of the six His codons is prevented and, therefore, thepolypeptide is produced with no 6×His tag.

The DNA sequence encoding the desired portion of the protein comprisingthe extracellular domain sequence is amplified from the deposited cDNAclone using PCR oligonucleotide primers which anneal to the aminoterminal sequences of the desired portion of the protein and tosequences in the deposited construct 3′ to the cDNA coding sequence.Additional nucleotides containing restriction sites to facilitatecloning in the pQE60 vector are added to the 5′ and 3′ sequences,respectively.

For cloning the extracellular domain of the protein, the 5′ primer hasthe sequence 5′-GTG TCA TGA GCC TCC GGG CAG AGC TG-3′ (SEQ ID NO:12)containing the underlined Bsp HI restriction site followed by 17nucleotides of the amino terminal coding sequence of the extracellulardomain of the sequence in FIGS. 1A and 1B. One of ordinary skill in theart would appreciate, of course, that the point in the protein codingsequence where the 5′ primer begins may be varied to amplify a desiredportion of the complete protein shorter or longer than the extracellulardomain of the form. The 3′ primer has the sequence 5′-GTG AAG CTT TTATTA CAG CAG TTT CAA TGC ACC-3′ (SEQ ID NO:13) containing the underlinedHind III restriction site followed by two stop codons and 18 nucleotidescomplementary to the 3′ end of the coding sequence in the DNA sequencein FIGS. 1A and 1B.

The amplified DNA fragments and the vector pQE60 are digested with BspHI and Hind III and the digested DNAs are then ligated together.Insertion of the DNA into the restricted pQE60 vector places the proteincoding region including its associated stop codon downstream from theIPTG-inducible promoter and in-frame with an initiating AUG. Theassociated stop codon prevents translation of the six histidine codonsdownstream of the insertion point.

The ligation mixture is transformed into competent E. coli cells usingstandard procedures such as those described in Sambrook et al.,Molecular Cloning: a Laboratory Manual, 2nd Ed.; Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (1989). E. coli strainM15/rep4, containing multiple copies of the plasmid pREP4, whichexpresses the lac repressor and confers kanamycin resistance(“Kan^(r)”), is used in carrying out the illustrative example describedherein. This strain, which is only one of many that are suitable forexpressing protein, is available commercially from QIAGEN, Inc., supra.Transformants are identified by their ability to grow on LB plates inthe presence of ampicillin and kanamycin. Plasmid DNA is isolated fromresistant colonies and the identity of the cloned DNA confirmed byrestriction analysis, PCR and DNA sequencing.

One of ordinary skill in the art recognizes that any of a number ofbacterial expression vectors may be useful in place of pQE9 and pQE60 inthe expression protocols presented in this example. For example, thenovel pHE4 series of bacterial expression vectors, in particular, thepHE4-5 vector may be used for bacterial expression in this example (ATCCAccession No. 209311; and variations thereof). The plasmid DNAdesignated pHE4-5/MPIFD23 in ATCC Deposit No. 209311 is vector plasmidDNA which contains an insert which encodes another ORF. The constructwas deposited with the American Type Culture Collection, 10801University Boulevard, Manassas, Va. 20110-2209, on Sep. 30, 1997. Usingthe Nde I and Asp 718 restriction sites flanking the irrelevant MPIF ORFinsert, one of ordinary skill in the art could easily use currentmolecular biological techniques to replace the irrelevant ORF in thepHE4-5 vector with the Neutrokine-alpha ORF of the present invention.

The pHE4-5 bacterial expression vector includes a neomycinphosphotransferase gene for selection, an E. coli origin of replication,a T5 phage promoter sequence, two lac operator sequences, aShine-Delgarno sequence, and the lactose operon repressor gene (lacIq).These elements are arranged such that an inserted DNA fragment encodinga polypeptide expresses that polypeptide with the six His residues(i.e., a “6×His tag”) covalently linked to the amino terminus of thatpolypeptide. The promoter and operator sequences of the pHE4-5 vectorwere made synthetically. Synthetic production of nucleic acid sequencesis well known in the art (CLONTECH 95/96 Catalog, pages 215-216,CLONTECH, 1020 East Meadow Circle, Palo Alto, Calif. 94303).

Clones containing the desired Neutrokine-alpha constructs are grownovernight (“O/N”) in liquid culture in LB media supplemented with bothampicillin (100 μg/ml) and kanamycin (25 μg/ml). The O/N culture is usedto inoculate a large culture, at a dilution of approximately 1:25 to1:250. The cells are grown to an optical density at 600 nm (“OD600”) ofbetween 0.4 and 0.6. isopropyl-beta-D-thiogalactopyranoside (“IPTG”) isthen added to a final concentration of 1 mM to induce transcription fromthe lac repressor sensitive promoter, by inactivating the lad repressor.Cells subsequently are incubated further for 3 to 4 hours. Cells thenare harvested by centrifugation.

The cells are then stirred for 3-4 hours at 4° C. in 6M guanidine-HCl,pH 8. The cell debris is removed by centrifugation, and the supernatantcontaining the Neutrokine-alpha is dialyzed against 50 mM Na-acetatebuffer pH 6, supplemented with 200 mM NaCl. Alternatively, the proteincan be successfully refolded by dialyzing it against 500 mM NaCl, 20%glycerol, 25 mM Tris/HCl pH 7.4, containing protease inhibitors. Afterrenaturation the protein can be purified by ion exchange, hydrophobicinteraction and size exclusion chromatography. Alternatively, anaffinity chromatography step such as an antibody column can be used toobtain pure protein. The purified protein is stored at 4° C. or frozenat −80° C.

In certain embodiments, it is preferred to generate expressionconstructs as detailed in this Example to mutate one or more of thethree cysteine residues in the Neutrokine-alpha polypeptide sequence.The cysteine residues in the Neutrokine-alpha polypeptide sequence arelocated at positions 147, 232, and 245 as shown in SEQ ID NO:2 and atpositions 213 and 226 of the Neutrokine-alpha polypeptide sequence asshown in SEQ ID NO:19 (there is no cysteine in the Neutrokine-alphaSVpolypeptide sequence which corresponds to Cys-147 in theNeutrokine-alpha polypeptide sequence because amino acid residues143-160 of the Neutrokine-alpha polypeptide sequence are not present inthe Neutrokine-alphaSV polypeptide sequence).

Example 2 Cloning, Expression, and Purification of Neutrokine-AlphaProtein in a Baculovirus Expression System

In this illustrative example, the plasmid shuttle vector pA2GP is usedto insert the cloned DNA encoding the extracellular domain of theprotein, lacking its naturally associated intracellular andtransmembrane sequences, into a baculovirus to express the extracellulardomain of the Neutrokine-alpha protein, using a baculovirus leader andstandard methods as described in Summers et al., A Manual of Methods forBaculovirus Vectors and Insect Cell Culture Procedures, TexasAgricultural Experimental Station Bulletin No. 1555 (1987). Thisexpression vector contains the strong polyhedrin promoter of theAutographa californica nuclear polyhedrosis virus (AcMNPV) followed bythe secretory signal peptide (leader) of the baculovirus gp67 proteinand convenient restriction sites such as Bam HI, Xba I and Asp 718. Thepolyadenylation site of the simian virus 40 (“SV40”) is used forefficient polyadenylation. For easy selection of recombinant virus, theplasmid contains the beta-galactosidase gene from E. coli under controlof a weak Drosophila promoter in the same orientation, followed by thepolyadenylation signal of the polyhedrin gene. The inserted genes areflanked on both sides by viral sequences for cell-mediated homologousrecombination with wild-type viral DNA to generate viable virus thatexpresses the cloned polynucleotide.

Many other baculovirus vectors could be used in place of the vectorabove, such as pAc373, pVL941 and pAcIM1, as one skilled in the artwould readily appreciate, as long as the construct providesappropriately located signals for transcription, translation, secretionand the like, including a signal peptide and an in-frame AUG asrequired. Such vectors are described, for instance, in Luckow et al.,Virology 170:31-39 (1989).

The cDNA sequence encoding an N-terminally deleted form of theextracellular domain of the Neutrokine-alpha protein in the depositedclone, lacking the AUG initiation codon, the naturally associatedintracellular and transmembrane domain sequences, and amino acids Gln-73through Leu-79 shown in FIGS. 1A and 1B (SEQ ID NO:2), is amplifiedusing PCR oligonucleotide primers corresponding to the 5′ and 3′sequences of the gene. The 5′ primer has the sequence 5′-GTG GGA TCC CCGGGC AGA GCT GCA GGG C-3′ (SEQ ID NO:14) containing the underlined Bam HIrestriction enzyme site followed by 18 nucleotides of the sequence ofthe extracellular domain of the Neutrokine-alpha protein shown in FIGS.1A and 1B, beginning with the indicated N-terminus of the extracellulardomain of the protein. The 3′ primer has the sequence 5′-GTG GGA TCC TTATTA CAG CAG TTT CAA TGC ACC-3′ (SEQ ID NO:15) containing the underlinedBam HI restriction site followed by two stop codons and 18 nucleotidescomplementary to the 3′ coding sequence in FIGS. 1A and 1B.

In certain other embodiments, constructs designed to express the entirepredicted extracellular domain of the Neutrokine-alpha (i.e., amino acidresidues Gln-73 through Leu-285) are preferred. One of skill in the artwould be able to use the polynucleotide and polypeptide sequencesprovided as SEQ ID NO:1 and SEQ ID NO:2, respectively, to designpolynucleotide primers to generate such a clone.

In a further preferred embodiment, a pA2GP expression construct encodesamino acid residues Leu-112 through Leu-285 of the Neutrokine-alphapolypeptide sequence shown as SEQ ID NO:2.

In another preferred embodiment, a pA2GP expression construct encodesamino acid residues Ser-78 through Leu-285 of the Neutrokine-alphapolypeptide sequence shown as SEQ ID NO:2.

The amplified fragment is isolated from a 1% agarose gel using acommercially available kit (“Geneclean,” BIO 101 Inc., La Jolla,Calif.). The fragment then is digested with Bam HI and again is purifiedon a 1% agarose gel. This fragment is designated herein F1.

The plasmid is digested with the restriction enzymes Bam HI andoptionally, can be dephosphorylated using calf intestinal phosphatase,using routine procedures known in the art. The DNA is then isolated froma 1% agarose gel using a commercially available kit (“Geneclean” BIO 101Inc., La Jolla, Calif.). This vector DNA is designated herein “V1”.

Fragment F1 and the dephosphorylated plasmid V1 are ligated togetherwith T4 DNA ligase. E. coli HB101 or other suitable E. coli hosts suchas XL-1 Blue (Statagene Cloning Systems, La Jolla, Calif.) cells aretransformed with the ligation mixture and spread on culture plates.Bacteria are identified that contain the plasmid with the human gene bydigesting DNA from individual colonies using Bam HI and then analyzingthe digestion product by gel electrophoresis. The sequence of the clonedfragment is confirmed by DNA sequencing. This plasmid is designatedherein pA2GP-Neutrokine-alpha.

Five micrograms of the plasmid pA2GP-Neutrokine-alpha is co-transfectedwith 1.0 microgram of a commercially available linearized baculovirusDNA (“BaculoGold™ baculovirus DNA”, Pharmingen, San Diego, Calif.),using the lipofection method described by Felgner et al., Proc. Natl.Acad. Sci. USA 84: 7413-7417 (1987). One μg of BaculoGold™ virus DNA and5 micrograms of the plasmid pA2GP Neutrokine-alpha are mixed in asterile well of a microtiter plate containing 50 microliters ofserum-free Grace's medium (Life Technologies Inc., Gaithersburg, Md.).Afterwards, 10 microliters Lipofectin plus 90 microliters Grace's mediumare added, mixed and incubated for 15 minutes at room temperature. Thenthe transfection mixture is added drop-wise to Sf9 insect cells (ATCCCRL 1711) seeded in a 35 mm tissue culture plate with 1 ml Grace'smedium without serum. The plate is then incubated for 5 hours at 27° C.The transfection solution is then removed from the plate and 1 ml ofGrace's insect medium supplemented with 10% fetal calf serum is added.Cultivation is then continued at 27° C. for four days.

After four days the supernatant is collected and a plaque assay isperformed, as described by Summers and Smith, supra. An agarose gel with“Blue Gal” (Life Technologies Inc., Rockville, Md.) is used to alloweasy identification and isolation of gal-expressing clones, whichproduce blue-stained plaques. (A detailed description of a “plaqueassay” of this type can also be found in the user's guide for insectcell culture and baculovirology distributed by Life Technologies Inc.,Rockville, Md., page 9-10). After appropriate incubation, blue stainedplaques are picked with the tip of a micropipettor (e.g., Eppendorf).The agar containing the recombinant viruses is then resuspended in amicrocentrifuge tube containing 200 microliters of Grace's medium andthe suspension containing the recombinant baculovirus is used to infectSf9 cells seeded in 35 mm dishes. Four days later the supernatants ofthese culture dishes are harvested and then they are stored at 4° C. Therecombinant virus is called V-Neutrokine-alpha.

To verify the expression of the Neutrokine-alpha gene Sf9 cells aregrown in Grace's medium supplemented with 10% heat-inactivated FBS. Thecells are infected with the recombinant baculovirus V-Neutrokine-alphaat a multiplicity of infection (“MOT”) of about 2. If radiolabeledproteins are desired, 6 hours later the medium is removed and isreplaced with SF900 II medium minus methionine and cysteine (availablefrom Life Technologies Inc., Rockville, Md.). After 42 hours, 5microcuries of ³⁵S-methionine and 5 microcuries ³⁵S-cysteine (availablefrom Amersham) are added. The cells are further incubated for 16 hoursand then are harvested by centrifugation. The proteins in thesupernatant as well as the intracellular proteins are analyzed bySDS-PAGE followed by autoradiography (if radiolabeled).

Microsequencing of the amino acid sequence of the amino terminus ofpurified protein may be used to determine the amino terminal sequence ofthe extracellular domain of the protein and thus the cleavage point andlength of the secretory signal peptide.

In a specific experimental example, recombinant Neutrokine-alpha waspurified from baculovirus infected Sf9 cell supernatants as follows. Theinsect cells were grown in EXCEL401 medium (JRH Scientific) with 1%(v/v) fetal bovine serum. At 92 hours post-infection, the harvestedsupernatant was clarified by centrifugation at 18,000×g followed by 0.45m depth filtration. A de-lipid filtration step might be also used toremove the lipid contaminants and in turn to improve initial capturingof the Neutrokine-alpha protein.

The supernatant was loaded on to a set of Poros HS-50/HQ-50 in tandemmode. As alternatives, Toyopearl QAE, Toyopearl Super Q (Tosohass),Q-Sepharose (Pharmacia) and equivalent resins might be used. This stepis used as a negative purification step to remove strong anion bindingcontaminants. The HS/HQ flow through material was adjusted to pH 7.5with 1 M Tris-HCl pH 8, diluted with equal volume of 50 mM Tris-HCl pH8, and loaded onto a poros PI-20 or PI-50 column. The PI column waswashed first with 4 column volumes of 75 mM sodium chloride in 50 mMTris-HCl at pH 7.5, then eluted using 3 to 5 column volumes of astepwise gradient of 300 mM, 750 mM, 1500 mM sodium chloride in 50 mMTris-HCl pH 7.5. Neutrokine-alpha protein appears as a 17 kDa band onreduced SDS-PAGE and is present in the 0.75 M to 1.5M Sodium chloridefractions.

The PI fraction was further purified through a Sephacryl S100 HR(Pharmacia) size exclusion column equilibrated with 0.15 M sodiumchloride, 50 mM sodium acetate at pH 6. The S200 fractions were mixedwith sodium chloride to a final concentration of 3 M and loaded onto aToyopearl Hexyl 650C (Tosohass) column. The Hexyl column was eluted witha linear gradient from 3 M to 0.05 M sodium chloride in 50 mM Sodiumacetate pH 6 in 5 to 15 column volumes. The sodium chloride gradient canalso be replaced by ammonium sulfate gradient of 1M to 0 M in 50 mMsodium acetate pH 6 in the Hexyl chromatographic step. Fractionscontaining purified Neutrokine-alpha as analyzed through SDS-PAGE werecombined and dialyzed against a buffer containing 150 mM Sodiumchloride, 50 mM Sodium acetate, pH 6.

The final purified Neutrokine-alpha protein expressed in a baculovirussystem as explained herein has an N-terminus sequence which begins withamino acid residue Ala-134 of SEQ ID NO:2. RP-HPLC analysis shows asingle peak of greater than 95% purity. Endotoxin level was below thedetection limit in LAL assay.

In another example, recombinant Neutrokine-alpha was purified frombaculovirus infected Sf9 cell supernatants containing 0.25% bovine serumas follows.

The Sf9 supernatant was harvested by centrifugation at 18,000×g. Thesupernatant was then treated with 10 mM calcium chloride in slightlyalkaline conditions for 10-15 minutes followed by centrifugation andthen 0.22 micrometer depth filtration. The resulting Sf-9 cellsupernatant was then diluted 2-fold and loaded on to a Poros PI-50column (available from PE Biosystems). The column was equilibrated with50 mM Tris (pH=7.4). The PI-50 column was washed with 1 CV of 50 mM Tris(pH=7.4) and then eluted with 1.5 M NaCl in 50 mM NaOAc (pH=6) over 3CV. The PI fraction was loaded on to a Sephacryl S200 columnequilibrated with 50 mM NaOAc (pH=6), 125 mM NaCl. The 5200 fraction wasmixed with salts to final concentrations of 0.7 M ammonium sulfate and0.6 M NaCl and loaded on to a Toyopearl Hexyl 650C column (availablefrom Toso Haas) that had been equilibrated in a buffer containing 0.6 MNaCl, 0.7 M ammonium sulfate in 50 mM NaOAc (pH=6). The column was thenwashed with 2 CV of the same buffer. Recombinant Neutrokine-alpha wasthen eluted stepwise with 3 CV of 50 mM NaOAc (pH=6) followed by 2 CV of20% ethanol wash. The recombinant Neutrokine-alpha protein was theneluted at the end of the ammonium sulfate (0.3 to 0 M salt) gradient.The appropriate fractions were pooled and dialyzed against a buffercontaining 50 mM NaOAc (pH=6), and then passed through a Poros 50 HQcolumn. The HQ flow-through was diluted to 4 ms and loaded on to aToyopearl DEAD 650M column and then eluted with 25 mM NaCitrate, 125 mMNaCl.

In another example, recombinant Neutrokine-alpha was expressed andpurified using a baculoviral vector system in Sf+ insect cells.

First, a polynucleotide encoding amino acid residues Ser-78 throughLeu-285 of the Neutrokine-alpha polypeptide sequence shown in FIGS. 1Aand 1B (which is exactly identical to amino acid residues Ser-78 throughLeu-285 of the Neutrokine-alpha polypeptide sequence shown as SEQ IDNO:2) was subcloned into the baculovirus transfer construct PSC togenerate a baculovirus expression plasmid. The pA2GP transfer vector,derived from pVL941, contains the gp67 signal peptide, a modifiedmultiple cloning site, and the lac Z gene cloned downstream of theDrosophila heat-shock promoter for selection of blue plaques. Using thesequence of Neutrokine-alpha (SEQ ID NO:2) and the sequence of the pA2GPvector, a cloning strategy was designed for seamlessly fusing the PSCsignal peptide coding sequence to the Neutrokine-alpha coding sequenceat Ala-134 (SEQ ID NO:2 and FIGS. 1A and 1B) and inserting it into a PSCbaculovirus transfer plasmid. The strategy involved the use of atwo-stage polymerase chain reaction (PCR) procedure. First, primers weredesigned for amplifying the Neutrokine-alpha sequences. The 5′ primerconsisted of the sequence encoding Ala-134 and following residues(5′-GGT CGC CGT TTC TAA CGC GGC CGT TCA GGG TCC AGA AG-3′; SEQ IDNO:31), preceded by the sequence encoding the PSC signal peptideC-terminus. The 3′ primer (5′-CTG GTT CGG CCC AAG GTA CCA AGC TTG TACCTT AGA TCT TTT CTA GAT C-3′; SEQ ID NO:32) consisted of the reversecomplement of the pA2GP vector sequence immediately downstream from theNeutrokine-alpha coding sequence, preceded by a Kpn I restrictionendonuclease site and a spacer sequence (for increased cuttingefficiency by Kpn I). PCR was performed with the pA2GP containingNeutrokine-alpha plasmid template and primers O-1887 and O-1888, and theresulting PCR product was purified using standard techniques.

An additional PCR reaction was performed using the PSC baculovirustransfer plasmid pMGS12 as a template. The pMGS12 plasmid consists ofthe AcNPV EcoRI “I” fragment inserted into pUC8, with the polyhedrincoding sequences after the ATG start codon replaced with the PSC signalpeptide and a polylinker site. The PCR reaction used pMGS12 as atemplate, a 5′ primer (5′-CTG GTA GTT CTT CGG AGT GTG-3′; SEQ ID NO:33)which annealed in AcNPV ORF603 upstream of the unique NgoM IV and EcoR Vsites, and a 3′ primer (5′-CGC GTT AGA AAC GGC GAC C-3′; SEQ ID NO:34)which annealed to the 3′ end of the sequence encoding the PSC signalpeptide.

To generate a PCR product in which the PSC signal peptide was seamlesslyfused to the Ala-134 of the Neutrokine-alpha coding sequence, the PCRproduct was combined with the PSC signal peptide-polyhedrin upstreamregion PCR product and subjected to an additional round of PCR. Becausethe 3′ end of the PSC signal peptide PCR product (pMGS12/O-959/O-1044)overlapped the 5′ end of the Neutrokine-alpha PCR product prepared withprimers O-1887/O-1888, the two PCR products were combined andoverlap-extended by PCR using primers O-959 and O-1888.

The resulting overlap-extended PCR product containing the PSC signalpeptide fused to the Neutrokine-alpha sequence subsequently was insertedinto baculovirus transfer plasmid pMGS12. The PCR product was digestedwith NgoM IV and Kpn I, and the fragment was purified and ligated intoNgoM IV-Kpn I-cut pMGS12. After transformation of competent E. coliDHSalpha cells with the ligation mix, colonies were picked and plasmidDNA mini-preps were prepared. Several positive clones from each ligationwere identified by restriction digestion analysis of the plasmid DNA,and three clones (pAcC9669, pAcC9671, and pAcC9672) were selected forlarge scale plasmid purification. The resulting plasmid DNA wassubjected to DNA sequence analysis to confirm and sequence theNeutrokine-alpha insert.

The following steps describe the recovery and purification process ofrecombinant Neutrokine-alpha from Sf+ insect cells. Unless statedotherwise, the process is conducted at 2-8° C.

Recovery

Step 1. CaCl₂ Treatment

Sf+ cell supernatant was harvested by centrifugation at 8,000×g.Recovery buffer-1 (1M CaCl₂) was added to the supernatant so that thefinal concentration of CaCl₂ was 10 mM. (In a further preferredembodiment, 1M ZnCl₂ is used in place of 1M CaCl₂.) The pH of thesolution was adjusted to 7.7±with Recovery buffer-2 (1M Tris pH 8(±0.2)). The solution was incubated for 15 minutes and then centrifugedat 8,000×g.

Purification

Step 1. Chromatography on Poros PI-50 Column

Sf+ cell supernatant was loaded on to a Poros PI-50 column (PEBiosystem). The column was equilibrated in PI-1 buffer (50 mM Tris, 50mM NaCl, pH 7.4 (±0.2)). The PI-50 column was washed with 1-2 CV of PI-1buffer and then eluted with PI-2 buffer (50 mM Na Citrate pH 6 (±0.2))over 3 CV linear gradient. The elution was monitored by ultraviolet (UV)absorbance at 280 nm. Fractions were collected across the eluate peakand analyzed by SDS page. Appropriate fractions were pooled.

Step 2. Chromatography on Toyopearl Hexyl 650C Column

The PI pool was mixed with salts to final concentrations of 0.7M(NH₄)₂SO₄ and loaded on to a Toyopearl Hexyl 650C (Toso Haas) columnequilibrated in HIC-1 buffer (50 mM NaOAc, 0.6M NaCl, 0.7M (NH₄)₂SO₄ pH6 (±0.2)). The column was then washed with 2 CV of HIC-1 buffer.Subsequently, recombinant Neutrokine-alpha was then eluted stepwise with3-5 CV of HIC-2 buffer (50 mM NaOAc pH 6.0 (±0.2)) followed by a 2 CV20% ethanol wash. The elution was monitored by UV absorbance at 280 nmand conductivity. Fractions were collected across the eluate peak andanalyzed by SDS-PAGE. The appropriate fractions were then pooled.

Step 3. Chromatography on SP Sepharose FF

The Hexyl fraction was dialyzed and adjusted to pH 4.5 with SP-1 buffer(50 mM sodium acetate pH 4.5 (±0.2)), diluted to 4 ms and loaded througha SP sepharose (cation exchanger, Pharmacia) column equilibrated withSP-1 buffer (50 mM sodium acetate pH 4.5 (±0.2)). RecombinantNeutrokine-alpha protein was then eluted from the SP column with SP-2buffer (50 mM sodium acetate pH 5.5 (±0.2)) at pH 5.5. The elution wasthen monitored by ultraviolet (UV) absorbance at 280 nm. Fractions werecollected across the eluate peak and analyzed by SDS page. Appropriatefractions were pooled.

Step 4. Dialysis of Recombinant Neutrokine-Alpha

The SP fractions were placed into a 6-8 kDa cutoff membrane device andthen dialyzed or diafiltered into Dialysis Buffer (10 mM sodium citrate,140 mM sodium chloride pH 6 (±0.2)) overnight.

Step 5. Filtration and Fill

The protein concentration of the recombinant Neutrokine-alpha solutionfrom Step 6 was determined by bicinchoninic acid (BCA) protein assay.Recombinant Neutrokine-alpha formulation was adjusted to the finalprotein concentration with the appropriate buffer and filtered undercontrolled conditions. The filtrate (bulk substance) was stored insuitable sterilized containers below −20° C.

In a specific embodiment, Neutrokine-alpha protein of the inventionproduced as described infra was adjusted to a final proteinconcentration of 1 to 5 mg/ml and buffered in 10 mM sodium citrate, 140mM sodium chloride, pH=6.0±(0.4) and stored at or below −20° C. in Type1 glass vials.

During chromatography runs, the processes are monitored by UV absorbanceat 280 nm. When applicable, in-process chromatography intermediates aretested for conductivity, pH, and monitored by SDS and/or RP-HPLC.

Columns and purification equipment are cleaned and sanitized with 0.2 or0.5 M NaOH followed by deionized water and then 0.1 or 0.5 M aceticacid. The column and purification equipment are rinsed with deionizedwater and, if necessary, stored in the appropriate storage solution.Prior to use, the equipment is equilibrated with appropriate buffers (asdescribed herein or as is well known in the art).

In a further preferred embodiment, 1M ZnCl₂ is used in place of 1M CaCl₂in Step 1 of the Recovery section described above. Also, in thisembodiment, a combination of ZnCl₂ and CaCl₂ may be used. Manycombinations of 0.1 M ZnCl₂ and 0.9 M CaCl₂, may be used in the Recoveryprocess of recombinant Neutrokine-alpha protein such as, for example,but not limited to, a combination of 0.1 M ZnCl₂ and 0.9 M CaCl₂, 0.2 MZnCl₂ and 0.8 M CaCl₂, 0.3 M ZnCl₂ and 0.7 M CaCl₂, 0.4 M ZnCl₂ and 0.6M CaCl₂, 0.5 M ZnCl₂ and 0.5 M CaCl₂, 0.6 M ZnCl₂ and 0.4 M CaCl₂, 0.7 MZnCl₂ and 0.3 M CaCl₂, 0.8 M ZnCl₂ and 0.2 M CaCl₂, 0.9 M ZnCl₂ and 0.1M CaCl₂, and others. However, the presence of EDTA will inhibit therecovery process. Moreover, the presence of ZnCl₂ and/or CaCl₂ inRecovery Buffer-1 will induce the formation of larger amounts of highermolecular weight (or molecular mass) Neutrokine-alpha multimers.

Example 3 Cloning and Expression of Neutrokine-Alpha in Mammalian Cells

A typical mammalian expression vector contains the promoter element,which mediates the initiation of transcription of mRNA, the proteincoding sequence, and signals required for the termination oftranscription and polyadenylation of the transcript. Additional elementsinclude enhancers, Kozak sequences and intervening sequences flanked bydonor and acceptor sites for RNA splicing. Highly efficienttranscription can be achieved with the early and late promoters fromSV40, the long terminal repeats (LTRs) from Retroviruses, e.g., RSV,HTLVI, HIVI and the early promoter of the cytomegalovirus (CMV).However, cellular elements can also be used (e.g., the human actinpromoter). Suitable expression vectors for use in practicing the presentinvention include, for example, vectors such as pSVL and pMSG(Pharmacia, Uppsala, Sweden), pRSVcat (ATCC 37152), pSV2dhfr (ATCC37146) and pBC12MI (ATCC 67109). Mammalian host cells that could be usedinclude, human HeLa, 293, H9 and Jurkat cells, mouse NIH3T3 and C127cells, Cos 1, Cos 7 and CV1, quail QC1-3 cells, mouse L cells, Chinesehamster ovary (CHO) cells, and HEK 293 cells.

Alternatively, the gene can be expressed in stable cell lines thatcontain the gene integrated into a chromosome. The co-transfection witha selectable marker such as dhfr, gpt, neomycin, hygromycin allows theidentification and isolation of the transfected cells.

The transfected gene can also be amplified to express large amounts ofthe encoded protein. The DHFR (dihydrofolate reductase) marker is usefulto develop cell lines that carry several hundred or even severalthousand copies of the gene of interest. Another useful selection markeris the enzyme glutamine synthase (GS) (Murphy et al., Biochem J.227:277-279 (1991); Bebbington et al., Bio/Technology 10:169-175(1992)). Using these markers, the mammalian cells are grown in selectivemedium and the cells with the highest resistance are selected. Thesecell lines contain the amplified gene(s) integrated into a chromosome.Chinese hamster ovary (CHO) and NSO cells are often used for theproduction of proteins.

The expression vectors pC1 and pC4 contain the strong promoter (LTR) ofthe Rous Sarcoma Virus (Cullen et al., Molecular and Cellular Biology,438-447 (March, 1985)) plus a fragment of the CMV-enhancer (Boshart etal., Cell 41:521-530 (1985)). Multiple cloning sites, e.g., with therestriction enzyme cleavage sites Bam HI, Xba I and Asp 718, facilitatethe cloning of the gene of interest. The vectors contain in addition the3′ intron, the polyadenylation and termination signal of the ratpreproinsulin gene.

Example 3(a) Cloning and Expression in COS Cells

The expression plasmid, pNeutrokine-alpha-HA, is made by cloning aportion of the deposited cDNA encoding the extracellular domain of theprotein into the expression vector pcDNAI/Amp or pcDNAIII (which can beobtained from Invitrogen, Inc.). To produce a soluble, secreted form ofthe polypeptide, the extracellular domain is fused to the secretoryleader sequence of the human IL-6 gene.

The expression vector pcDNAI/amp contains: (1) an E. coli origin ofreplication effective for propagation in E. coli and other prokaryoticcells; (2) an ampicillin resistance gene for selection ofplasmid-containing prokaryotic cells; (3) an SV40 origin of replicationfor propagation in eukaryotic cells; (4) a CMV promoter, a polylinker,an SV40 intron; (5) several codons encoding a hemagglutinin fragment(i.e., an “HA” tag to facilitate purification) followed by a terminationcodon and polyadenylation signal arranged so that a cDNA can beconveniently placed under expression control of the CMV promoter andoperably linked to the SV40 intron and the polyadenylation signal bymeans of restriction sites in the polylinker. The HA tag corresponds toan epitope derived from the influenza hemagglutinin protein described byWilson et al., Cell 37: 767 (1984). The fusion of the HA tag to thetarget protein allows easy detection and recovery of the recombinantprotein with an antibody that recognizes the HA epitope. pcDNAIIIcontains, in addition, the selectable neomycin marker.

A DNA fragment encoding the extracellular domain of the Neutrokine-alphapolypeptide is cloned into the polylinker region of the vector so thatrecombinant protein expression is directed by the CMV promoter. Theplasmid construction strategy is as follows. The Neutrokine-alpha cDNAof the deposited clone is amplified using primers that containconvenient restriction sites, much as described above for constructionof vectors for expression of Neutrokine-alpha in E. coli. Suitableprimers include the following, which are used in this example. The 5′primer, containing the underlined Bam HI site, a Kozak sequence, an AUGstart codon, a sequence encoding the secretory leader peptide from thehuman IL-6 gene, and 18 nucleotides of the 5′ coding region of theextracellular domain of Neutrokine-alpha protein, has the followingsequence: 5′-GCG GGA TCC GCC ACC ATG AAC TCC TTC TCC ACA AGC GCC TTC GGTCCA GTT GCC TTC TCC CTG GGG CTG CTC CTG GTG TTG CCT GCT GCC TTC CCT GCCCCA GTT GTG AGA CAA GGG GAC CTG GCC AGC-3′ (SEQ ID NO:16). The 3′primer, containing the underlined Bam HI restriction site and 18 ofnucleotides complementary to the 3′ coding sequence immediately beforethe stop codon, has the following sequence: 5′-GTG GGA TCC TTA CAG CAGTTT CAA TGC ACC-3′ (SEQ ID NO:17).

The PCR amplified DNA fragment and the vector, pcDNAI/Amp, are digestedwith Bam HI and then ligated. The ligation mixture is transformed intoE. coli strain SURE (available from Stratagene Cloning Systems, 11099North Torrey Pines Road, La Jolla, Calif. 92037), and the transformedculture is plated on ampicillin media plates which then are incubated toallow growth of ampicillin resistant colonies. Plasmid DNA is isolatedfrom resistant colonies and examined by restriction analysis or othermeans for the presence of the fragment encoding the Neutrokine-alphaextracellular domain.

For expression of recombinant Neutrokine-alpha, COS cells aretransfected with an expression vector, as described above, usingDEAE-DEXTRAN, as described, for instance, in Sambrook et al., MolecularCloning: a Laboratory Manual, Cold Spring Laboratory Press, Cold SpringHarbor, N.Y. (1989). Cells are incubated under conditions for expressionof Neutrokine-alpha by the vector.

Expression of the Neutrokine-alpha-HA fusion protein is detected byradiolabeling and immunoprecipitation, using methods described in, forexample Harlow et al., Antibodies: A Laboratory Manual, 2nd Ed.; ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1988). To thisend, two days after transfection, the cells are labeled by incubation inmedia containing ³⁵S-cysteine for 8 hours. The cells and the media arecollected, and the cells are washed and the lysed withdetergent-containing RIPA buffer: 150 mM NaCl, 1% NP-40, 0.1% SDS, 1%NP-40, 0.5% DOC, 50 mM TRIS, pH 7.5, as described by Wilson et al. citedabove. Proteins are precipitated from the cell lysate and from theculture media using an HA-specific monoclonal antibody. The precipitatedproteins then are analyzed by SDS-PAGE and autoradiography. Anexpression product of the expected size is seen in the cell lysate,which is not seen in negative controls.

Example 3(b) Cloning and Expression in CHO Cells

The vector pC4 is used for the expression of Neutrokine-alpha protein.Plasmid pC4 is a derivative of the plasmid pSV2-dhfr (ATCC Accession No.37146). To produce a soluble, secreted form of the Neutrokine-alphapolypeptide, the portion of the deposited cDNA encoding theextracellular domain is fused to the secretory leader sequence of thehuman IL-6 gene. The vector plasmid contains the mouse DHFR gene undercontrol of the SV40 early promoter. Chinese hamster ovary- or othercells lacking dihydrofolate activity that are transfected with theseplasmids can be selected by growing the cells in a selective medium(alpha minus MEM, Life Technologies) supplemented with thechemotherapeutic agent methotrexate. The amplification of the DHFR genesin cells resistant to methotrexate (MTX) has been well documented (see,e.g., Alt, F. W., Kellems, R. M., Bertino, J. R., and Schimke, R. T.,1978, J. Biol. Chem. 253:1357-1370, Hamlin, J. L. and Ma, C. 1990,Biochem. et Biophys. Acta, 1097:107-143, Page, M. J. and Sydenham, M. A.1991, Biotechnology 9:64-68). Cells grown in increasing concentrationsof MTX develop resistance to the drug by overproducing the targetenzyme, DHFR, as a result of amplification of the DHFR gene. If a secondgene is linked to the DHFR gene, it is usually co-amplified andover-expressed. It is known in the art that this approach may be used todevelop cell lines carrying more than 1,000 copies of the amplifiedgene(s). Subsequently, when the methotrexate is withdrawn, cell linesare obtained which contain the amplified gene integrated into one ormore chromosome(s) of the host cell.

Plasmid pC4 contains for expressing the gene of interest the strongpromoter of the long terminal repeat (LTR) of the Rouse Sarcoma Virus(Cullen, et al., Molecular and Cellular Biology, March 1985:438-447)plus a fragment isolated from the enhancer of the immediate early geneof human cytomegalovirus (CMV) (Boshart et al., Cell 41:521-530 (1985)).Downstream of the promoter are the following single restriction enzymecleavage sites that allow the integration of the genes: BamHI, Xba I,and Asp718. Behind these cloning sites the plasmid contains the 3′intron and polyadenylation site of the rat preproinsulin gene. Otherhigh efficiency promoters can also be used for the expression, e.g., thehuman beta-actin promoter, the SV40 early or late promoters or the longterminal repeats from other retroviruses, e.g., HIV and HTLVI.Clontech's Tet-Off and Tet-On gene expression systems and similarsystems can be used to express the Neutrokine-alpha in a regulated wayin mammalian cells (Gossen, M., & Bujard, H.1992, Proc. Natl. Acad. Sci.USA 89: 5547-5551). For the polyadenylation of the mRNA other signals,e.g., from the human growth hormone or globin genes can be used as well.Stable cell lines carrying a gene of interest integrated into thechromosomes can also be selected upon co-transfection with a selectablemarker such as gpt, G418 or hygromycin. It is advantageous to use morethan one selectable marker in the beginning, e.g., G418 plusmethotrexate.

The plasmid pC4 is digested with the restriction enzymes Bam HI and thendephosphorylated using calf intestinal phosphates by procedures known inthe art. The vector is then isolated from a 1% agarose gel.

The DNA sequence encoding the extracellular domain of theNeutrokine-alpha protein is amplified using PCR oligonucleotide primerscorresponding to the 5′ and 3′ sequences of the gene. The 5′ primer,containing the underlined Bam HI site, a Kozak sequence, an AUG startcodon, a sequence encoding the secretory leader peptide from the humanIL-6 gene, and 18 nucleotides of the 5′ coding region of theextracellular domain of Neutrokine-alpha protein, has the followingsequence: 5′-GCG GGA TCC GCC ACC ATG AAC TCC TTC TCC ACA AGC GCC TTC GGTCCA GTT GCC TTC TCC CTG GGG CTG CTC CTG GTG TTG CCT GCT GCC TTC CCT GCCCCA GTT GTG AGA CAA GGG GAC CTG GCC AGC-3′ (SEQ ID NO:16). The 3′primer, containing the underlined Bam HI and 18 of nucleotidescomplementary to the 3′ coding sequence immediately before the stopcodon, has the following sequence: 5′-GTG GGA TCC TTA CAG CAG TTT CAATGC ACC-3′ (SEQ ID NO:17).

The amplified fragment is digested with the endonuclease Bam HI and thenpurified again on a 1% agarose gel. The isolated fragment and thedephosphorylated vector are then ligated with T4 DNA ligase. E. coliHB101 or XL-1 Blue cells are then transformed and bacteria areidentified that contain the fragment inserted into plasmid pC4 using,for instance, restriction enzyme analysis.

Chinese hamster ovary cells lacking an active DHFR gene are used fortransfection. Five μg of the expression plasmid pC4 is cotransfectedwith 0.5 μg of the plasmid pSVneo using lipofectin (Felgner et al.,supra). The plasmid pSV2-neo contains a dominant selectable marker, theneo gene from Tn5 encoding an enzyme that confers resistance to a groupof antibiotics including G418. The cells are seeded in alpha minus MEMsupplemented with 1 mg/ml G418. After 2 days, the cells are trypsinizedand seeded in hybridoma cloning plates (Greiner, Germany) in alpha minusMEM supplemented with 10, 25, or 50 ng/ml of metothrexate plus 1 mg/mlG418. After about 10-14 days single clones are trypsinized and thenseeded in 6-well petri dishes or 10 ml flasks using differentconcentrations of methotrexate (50 nM, 100 nM, 200 nM, 400 nM, 800 nM).Clones growing at the highest concentrations of methotrexate are thentransferred to new 6-well plates containing even higher concentrationsof methotrexate (1 μM, 2 μM, 5 μM, 10 μM, 20 μM). The same procedure isrepeated until clones are obtained which grow at a concentration of100-200 μM. Expression of the desired gene product is analyzed, forinstance, by SDS-PAGE and Western blot or by reversed phase HPLCanalysis.

At least six Neutrokine-alpha expression constructs have been generatedby the inventors herein to facilitate the production of Neutrokine-alphaand/or Neutrokine-alphaSV polypeptides of several sizes and in severalsystems. The expression constructs are as follows: (1) pNa.A71-L285(expresses amino acid residues Ala-71 through Leu-285), (2) pNa.A81-L285(expresses amino acid residues Ala-81 through Leu-285), (3)pNa.L112-L285 (expresses amino acid residues Leu-112 through Leu-285),(4) pNa.A134-L285 (expresses amino acid residues Ala-134 throughLeu-285), (5) pNa.L147-L285 (expresses amino acid residues Leu-147through Leu-285), and (6) pNa.G161-L285 (expresses amino acid residuesGly-161 through Leu-285).

In preferred embodiments, the expression constructs are used to expressvarious Neutrokine-alpha muteins from bacterial, baculoviral, andmammalian systems.

In certain additional preferred embodiments, the constructs express aNeutrokine-alpha polypeptide fragment fused at the N- and/or C-terminusto a heterologous polypeptide, e.g., the signal peptide from human IL-6,the signal peptide from CK-beta8 (amino acids −21 to −1 of the CK-beta8sequence disclosed in published PCT application PCT/US95/09058), or thehuman IgG Fc region. Other sequences could be used which are known tothose of skill in the art.

Example 4 Tissue Distribution of Neutrokine-Alpha mRNA Expression

Northern blot analysis is carried out to examine Neutrokine-alpha geneexpression in human tissues, using methods described by, among others,Sambrook et al., cited above. A cDNA probe containing the entirenucleotide sequence of the Neutrokine-alpha protein (SEQ ID NO:1) islabeled with ³²P using the Rediprime™ DNA labeling system (Amersham LifeScience), according to manufacturer's instructions. After labeling, theprobe is purified using a CHROMA SPIN-100™ column (ClontechLaboratories, Inc.), according to manufacturer's protocol numberPT1200-1. The purified labeled probe is then used to examine varioushuman tissues for Neutrokine-alpha and/or Neutrokine-alpha mRNA.

Multiple Tissue Northern (MTN) blots containing various human tissues(H) or human immune system tissues (IM) are obtained from Clontech andare examined with the labeled probe using ExpressHyb™ hybridizationsolution (Clontech) according to manufacturer's protocol numberPT1190-1. Following hybridization and washing, the blots are mounted andexposed to film at −70° C. overnight, and films developed according tostandard procedures.

To determine the pattern of Neutrokine-alpha and/or Neutrokine-alphaexpression a panel of multiple tissue Northern blots were probed. Thisrevealed predominant expression of single 2.6 kb mRNA in peripheralblood leukocytes, spleen, lymph node and bone marrow, and detectableexpression in placenta, heart, lung, fetal liver, thymus and pancreas.Analysis of a panel of cell lines demonstrated high expression ofNeutrokine-alpha and/or Neutrokine-alpha in HL60 cells, detectableexpression in K562, but no expression in Raji, HeLa, or MOLT-4 cells.Overall it appears that Neutrokine-alpha and/or Neutrokine-alpha mRNAexpression is enriched in the immune system.

Example 5 Gene Therapy Using Endogenous Neutrokine-Alpha Gene

Another method of gene therapy according to the present inventioninvolves operably associating the endogenous Neutrokine-alpha sequencewith a promoter via homologous recombination as described, for example,in U.S. Pat. No. 5,641,670, issued Jun. 24, 1997; InternationalPublication No. WO 96/29411, published Sep. 26, 1996; InternationalPublication No. WO 94/12650, published Aug. 4, 1994; Koller et al.,Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); and Zijlstra et al.,Nature 342:435-438 (1989). This method involves the activation of a genewhich is present in the target cells, but which is not expressed in thecells, or is expressed at a lower level than desired. Polynucleotideconstructs are made which contain a promoter and targeting sequences,which are homologous to the 5′ non-coding sequence of endogenousNeutrokine-alpha, flanking the promoter. The targeting sequence will besufficiently near the 5′ end of Neutrokine-alpha so the promoter will beoperably linked to the endogenous sequence upon homologousrecombination. The promoter and the targeting sequences can be amplifiedusing PCR. Preferably, the amplified promoter contains distinctrestriction enzyme sites on the 5′ and 3′ ends. Preferably, the 3′ endof the first targeting sequence contains the same restriction enzymesite as the 5′ end of the amplified promoter and the 5′ end of thesecond targeting sequence contains the same restriction site as the 3′end of the amplified promoter.

The amplified promoter and the amplified targeting sequences aredigested with the appropriate restriction enzymes and subsequentlytreated with calf intestinal phosphatase. The digested promoter anddigested targeting sequences are added together in the presence of T4DNA ligase. The resulting mixture is maintained under conditionsappropriate for ligation of the two fragments. The construct is sizefractionated on an agarose gel then purified by phenol extraction andethanol precipitation.

In this Example, the polynucleotide constructs are administered as nakedpolynucleotides via electroporation. However, the polynucleotideconstructs may also be administered with transfection-facilitatingagents, such as liposomes, viral sequences, viral particles,precipitating agents, etc. Such methods of delivery are known in theart.

Once the cells are transfected, homologous recombination will take placewhich results in the promoter being operably linked to the endogenousNeutrokine-alpha sequence. This results in the expression ofNeutrokine-alpha in the cell. Expression may be detected byimmunological staining, or any other method known in the art.

Fibroblasts are obtained from a subject by skin biopsy. The resultingtissue is placed in DMEM+10% fetal calf serum. Exponentially growing orearly stationary phase fibroblasts are trypsinized and rinsed from theplastic surface with nutrient medium. An aliquot of the cell suspensionis removed for counting, and the remaining cells are subjected tocentrifugation. The supernatant is aspirated and the pellet isresuspended in 5 ml of electroporation buffer (20 mM HEPES pH 7.3, 137mM NaCl, 5 mM KCl, 0.7 mM Na2 HPO4, 6 mM dextrose). The cells arerecentrifuged, the supernatant aspirated, and the cells resuspended inelectroporation buffer containing 1 mg/ml acetylated bovine serumalbumin. The final cell suspension contains approximately 3×10⁶cells/ml. Electroporation should be performed immediately followingresuspension.

Plasmid DNA is prepared according to standard techniques. For example,to construct a plasmid for targeting to the Neutrokine-alpha locus,plasmid pUC18 (MBI Fermentas, Amherst, N.Y.) is digested with HindIII.The CMV promoter is amplified by PCR with an XbaI site on the 5′ end anda BamHI site on the 3′ end. Two Neutrokine-alpha non-coding sequencesare amplified via PCR: one Neutrokine-alpha non-coding sequence(Neutrokine-alpha fragment 1) is amplified with a HindIII site at the 5′end and an Xba site at the 3′ end; the other Neutrokine-alpha non-codingsequence (Neutrokine-alpha fragment 2) is amplified with a BamHI site atthe 5′ end and a HindIII site at the 3′ end. The CMV promoter andNeutrokine-alpha fragments are digested with the appropriate enzymes(CMV promoter—XbaI and BamHI; Neutrokine-alpha fragment 1-XbaI;Neutrokine-alpha fragment 2-BamHI) and ligated together. The resultingligation product is digested with HindIII, and ligated with theHindIII-digested pUC18 plasmid.

Plasmid DNA is added to a sterile cuvette with a 0.4 cm electrode gap(Bio-Rad). The final DNA concentration is generally at least 120 μg/ml.0.5 ml of the cell suspension (containing approximately 1.5.×106 cells)is then added to the cuvette, and the cell suspension and DNA solutionsare gently mixed. Electroporation is performed with a Gene-Pulserapparatus (Bio-Rad). Capacitance and voltage are set at 960 μF and250-300 V, respectively. As voltage increases, cell survival decreases,but the percentage of surviving cells that stably incorporate theintroduced DNA into their genome increases dramatically. Given theseparameters, a pulse time of approximately 14-20 mSec should be observed.

Electroporated cells are maintained at room temperature forapproximately 5 min, and the contents of the cuvette are then gentlyremoved with a sterile transfer pipette. The cells are added directly to10 ml of prewarmed nutrient media (DMEM with 15% calf serum) in a 10 cmdish and incubated at 37° C. The following day, the media is aspiratedand replaced with 10 ml of fresh media and incubated for a further 16-24hours.

The engineered fibroblasts are then injected into the host, either aloneor after having been grown to confluence on cytodex 3 microcarrierbeads. The fibroblasts now produce the protein product. The fibroblastscan then be introduced into a patient as described above.

Example 6 Neutrokine-Alpha, a Novel Member of the Tumor Necrosis FactorLigand Family that Functions as a B Lymphocyte Stimulator

A 285 amino acid protein was identified in a humanneutrophil/monocyte-derived cDNA library that shared significanthomology within its predicted extracellular receptor-ligand bindingdomain to APRIL (28.7%) (Hahne, M., et al., J. Exp. Med. 188, 1185-90(1998)), TNF-alpha (16.2%) (Pennica, D., et al., Nature 312, 724-729(1984)) and LT-alpha (14.1%) (Gray, Nature 312, 721-724 (1984)) (FIGS.7A-1 and 7A-2). We have designated this cytokine Neutrokine-alpha (wehave also designated this molecule as B Lymphocyte Stimulator (BLyS)based on its biological activity). Hydrophobicity analyses of theNeutrokine-alpha protein sequence have revealed a potentialtransmembrane spanning domain between amino acid residues 47 and 73which is preceded by non-hydrophobic amino acids suggesting thatNeutrokine-alpha, like other members of the TNF ligand family, is a typeII membrane bound protein (Cosman, D. Stem. Cells. 12:440-55 (1994)).Expression of this cDNA in mammalian cells (HEK 293 and Chinese HamsterOvary) and Sf9 insect cells identified a 152 amino acid soluble formwith an N-terminal sequence beginning with the alanine residue at aminoacid 134 (arrow in FIGS. 7A-1 and 7A-2). Reconstruction of the mass tocharge ratio defined a mass for Neutrokine-alpha of 17,038 Daltons, avalue in consistent with that predicted for this 152 amino acid proteinwith a single disulfide bond (17037.5 Daltons).

Using human/hamster somatic cell hybrids and a radiation-hybrid mappingpanel, the gene encoding Neutrokine-alpha was found linked to markerSHGC-36171 which maps to human chromosome 13q34, a region not previouslyassociated with any other member of the TNF superfamily of genes(Cosman, D. Stem. Cells. 12:440-55 (1994)).

The expression profile of Neutrokine-alpha was assessed by Northern blot(FIG. 7B) and flow cytometric analyses (Table V and FIGS. 8A, 8B, and8C). Neutrokine-alpha is encoded by a single 2.6 kb mRNA found at highlevels in peripheral blood leukocytes, spleen, lymph node and bonemarrow. Lower expression levels were detected in placenta, heart, lung,fetal liver, thymus and pancreas. Among a panel of cell lines,Neutrokine-alpha mRNA was detected in HL-60 and K562, but not in Raji,HeLa, or MOLT-4 cells. These results were confirmed by flow cytometricanalyses using the Neutrokine-alpha-specific mAb 2E5. As shown in TableV, Neutrokine-alpha expression is not detected on T or B lineage cellsbut rather restricted to cells within the myeloid origin. Furtheranalyses of normal blood cell types demonstrated significant expressionon resting monocytes that was upregulated approximately 4-fold followingexposure of cells to IFN-gamma (100 U/mL) for three days (FIGS. 8A and8B). A concomitant increase in Neutrokine-alpha-specific mRNA was alsodetected (FIG. 8C). By contrast, Neutrokine-alpha was not expressed onfreshly isolated peripheral blood granulocytes, T cells, B cells, or NKcells.

Purified recombinant Neutrokine-alpha (“rNeutrokine-alpha”) was assessedfor its ability to induce activation, proliferation, differentiation ordeath in numerous cell based assays involving B cells, T cells,monocytes, NK cells, hematopoietic progenitors, and a variety of celltypes of endothelial and epithelial origin. Among these assays,Neutrokine-alpha was specifically found to increase B cell proliferationin a standard co-stimulatory assay in which purified tonsillar B cellsare cultured in the presence of either formalin-fixed Staphylococcusaureus Cowan I (SAC) or immobilized anti-human IgM as priming agents(Sieckmann, D. G., et al., J. Exp. Med. 147:814-29 (1978); Ringden, 0.,et al., Scand. J. Immunol. 6:1159-69 (1977)). As shown in FIG. 9A,recombinant Neutrokine-alpha induced a dose-dependent proliferation oftonsillar B cells. This response was similar to that of rIL2 over thedose range from 0.1 to 10,000 ng/mL. Neutrokine-alpha also induces Bcell proliferation when cultured with cells co-stimulated withimmobilized anti-IgM (FIG. 9B). A dose-dependent response is readilyobserved as the amount of crosslinking agent increases in the presenceof a fixed concentration of either IL2 or rNeutrokine-alpha.

In an attempt to correlate the specific biological activity on B cellswith receptor expression, purified Neutrokine-alpha was biotinylated.The resultant biotin-Neutrokine-alpha protein retained biologicalfunction in the standard B cell proliferation assays. Lineage-specificanalyses of whole human peripheral blood cells indicated that binding ofbiotinylated Neutrokine-alpha was undetectable on T cells, monocytes, NKcells and granulocytes as assessed by CD3, CD14, CD56, and CD66brespectively (FIGS. 10A, 10B, 10C, 10D and 10E). In contrast,biotinylated Neutrokine-alpha bound peripheral CD20⁺ B cells. Receptorexpression was also detected on the B cell tumor lines REH, ARH-77,Raji, Namalwa, RPMI 8226, and IM-9 but not any of the myeloid-derivedlines tested including THP-1, HL-60, K-562, and U-937. Representativeflow cytometric profiles for the myeloma cell line IM-9 and thehistiocytic line U-937 are shown in FIGS. 10F and 10G. Similar resultswere also obtained using a biologically active FLAG-taggedNeutrokine-alpha protein instead of the chemically modifiedbiotin-Neutrokine-alpha. Taken together, these results confirm thatNeutrokine-alpha displays a clear B cell tropism in both its receptordistribution and biological activity. It remains to be shown whethercellular activation may induce expression of Neutrokine-alpha receptorson peripheral blood cells, other normal cell types or established celllines.

To examine the species specificity of Neutrokine-alpha, mouse splenic Bcells were cultured in the presence of human Neutrokine-alpha and SAC.Results demonstrate that rNeutrokine-alpha induced in vitroproliferation of murine splenic B cells and bound to a cell surfacereceptor on these cells. Interestingly, immature surface Ig negative Bcell precursors isolated from mouse bone marrow did not proliferate inresponse to Neutrokine-alpha nor did they bind the ligand.

To assess the in vivo activity of rNeutrokine-alpha, BALB/c mice(3/group) were injected (i.p.) twice per day with buffer only, or 0.08mg/kg, 0.8 mg/kg, 2 mg/kg or 8 mg/kg of rNeutrokine-alpha. Mice receivedthis treatment for 4 consecutive days at which time they were sacrificedand various tissues and serum collected for analyses. In an alternativeembodiment, BALB/c mice may be injected (i.p.) twice per day with anyamount of rNeutrokine-alpha in a range of 0.01 to 10 mg/kg. In apreferred embodiment, BALB/c mice are injected (i.p.) twice per day withany amount of rNeutrokine-alpha in a range of 0.01 to 3 mg/kg (specificpreferred exemplary dosages in this embodiment include, but are notlimited to, 0.01 mg/kg, 0.02 mg/kg, 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg,0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg, 0.1 mg/kg, 0.2 mg/kg,0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9mg/kg, 1.0 mg/kg, 1.1 mg/kg, 1.2 mg/kg, 1.3 mg/kg, 1.4 mg/kg, 1.5 mg/kg,1.6 mg/kg, 1.6 mg/kg, 1.7 mg/kg, 1.8 mg/kg, 1.9 mg/kg, 2.0 mg/kg, 2.1mg/kg, 2.2 mg/kg, 2.3 mg/kg, 2.4 mg/kg, 2.5 mg/kg, 2.6 mg/kg, 2.7 mg/kg,2.8 mg/kg, 2.9 mg/kg, and 3.0 mg/kg). In an additional preferredembodiment, BALB/c mice are injected (i.p.) twice per day with anyamount of rNeutrokine-alpha in a range of 0.02 to 2 mg/kg (specificpreferred exemplary dosages in this embodiment include, but are notlimited to, 0.02 mg/kg, 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg,0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg, 0.1 mg/kg, 0.2 mg/kg, 0.3 mg/kg, 0.4mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9 mg/kg, 1.0 mg/kg,1.1 mg/kg, 1.2 mg/kg, 1.3 mg/kg, 1.4 mg/kg, 1.5 mg/kg, 1.6 mg/kg, 1.6mg/kg, 1.7 mg/kg, 1.8 mg/kg, 1.9 mg/kg, and 2.0 mg/kg).

Microscopically, the effects of Neutrokine-alpha administration wereclearly evident in sections of spleen stained with routine hematoxylinand eosin (H&E) and immunohistochemically with a mAb specific forCD45R(B220) (FIG. 11A). Normal splenic architecture was altered by adramatic expansion of the white pulp marginal zone and a distinctincrease in cellularity of the red pulp (FIG. 11A). Marginal zoneexpansion appeared to be the result of increased numbers of lymphocytesexpressing the B cell marker CD45R(B220). In addition, the T cell denseperiarteriolar lymphoid sheath (PALS) areas were also infiltrated bymoderate numbers of CD45R(B220) positive cells. This suggests the whitepulp changes were due to increased numbers of B cells. The denselypacked cell population that frequently filled red pulps spaces did notstain with CD45R(B220). Additional experiments will be required tocharacterize all the cell types involved and further define themechanism by which Neutrokine-alpha alters splenic architecture.

Flow cytometric analyses of the spleens from mice treated with 2 mg/kgNeutrokine-alpha-treated indicated that Neutrokine-alpha increased theproportion of mature (CD45R(B220)^(dull), ThB^(bright)) B cellsapproximately 10-fold over that observed in control mice (FIGS. 11B and11C). Further analyses performed in which mice were treated with buffer,0.08 mg/kg, 0.8 mg/kg, 2 mg/kg, or 8 mg/kg Neutrokine-alpha indicatedthat 0.08 mg/kg, 0.8 mg/kg, and 2 mg/kg each increased the proportion ofmature (CD45R(B220)^(dull), ThB^(bright)) B cells approximately 10-foldover that observed in control mice, whereas buffer and 8 mg/kg producedapproximately equal proportions of mature B cells. See, Table IV.

TABLE IV FACS Analysis of Mouse Spleen B cell Population.Neutrokine-alpha (mg/kg) % Mature B Cells (R2) % CD45R-positive (R1)Control (buffer) 1.26 52.17 0.08 mg/kg   16.15 56.53 0.8 mg/kg   18.5457.56 2 mg/kg 16.54 57.55 8 mg/kg 1.24 61.42

A potential consequence of increased mature B cell representation invivo is a relative increase in serum Ig titers. Accordingly, serum IgA,IgG and IgM levels were compared between buffer andNeutrokine-alpha-treated mice (FIGS. 11D, 11E, and 11F).Neutrokine-alpha administration resulted in a 2- and 5-fold increase inIgA and IgM serum levels respectively. Interestingly, circulating levelsof IgG did not increase.

Moreover, a dose-dependent response was observed in serum IgA titers inmice treated with various amounts of Neutrokine-alpha over a period offour days, whereas no apparent dose-dependency was observed byadministration of the same amounts of Neutrokine-alpha over a period oftwo days. In the case of administration over four days, administrationof 8, 2, 0.8, 0.08, and 0 mg/kg Neutrokine-alpha resulted in serum IgAtiters of approximately 800 micrograms/ml, 700 micrograms/ml, 400micrograms/ml, 200 micrograms/ml and 200 micrograms/ml. That is,administration of 8, 2, 0.8, and 0.08 mg/kg Neutrokine-alpha over fourdays resulted in approximately 4-fold, 3.75-fold, 2-fold, andminimal-fold, respectively, increases in IgA serum levels overbackground or basal levels observed by administration of buffer only. Inan alternative embodiment, these experiments may be performed with anyamount of rNeutrokine-alpha in a range of 0.01 to 10 mg/kg. In apreferred embodiment, Neutrokine-alpha is administered in a range of0.01 to 3 mg/kg (specific preferred exemplary dosages in this embodimentinclude, but are not limited to, 0.01 mg/kg, 0.02 mg/kg, 0.03 mg/kg,0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg,0.1 mg/kg, 0.2 mg/kg, 0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7mg/kg, 0.8 mg/kg, 0.9 mg/kg, 1.0 mg/kg, 1.1 mg/kg, 1.2 mg/kg, 1.3 mg/kg,1.4 mg/kg, 1.5 mg/kg, 1.6 mg/kg, 1.6 mg/kg, 1.7 mg/kg, 1.8 mg/kg, 1.9mg/kg, 2.0 mg/kg, 2.1 mg/kg, 2.2 mg/kg, 2.3 mg/kg, 2.4 mg/kg, 2.5 mg/kg,2.6 mg/kg, 2.7 mg/kg, 2.8 mg/kg, 2.9 mg/kg, and 3.0 mg/kg). In anadditional preferred embodiment, Neutrokine-alpha is administered in arange of 0.02 to 2 mg/kg (specific preferred exemplary dosages in thisembodiment include, but are not limited to, 0.02 mg/kg, 0.03 mg/kg, 0.04mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg, 0.1mg/kg, 0.2 mg/kg, 0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg,0.8 mg/kg, 0.9 mg/kg, 1.0 mg/kg, 1.1 mg/kg, 1.2 mg/kg, 1.3 mg/kg, 1.4mg/kg, 1.5 mg/kg, 1.6 mg/kg, 1.6 mg/kg, 1.7 mg/kg, 1.8 mg/kg, 1.9 mg/kg,and 2.0 mg/kg).

The data presented herein define Neutrokine-alpha, as a novel member ofthe TNF-ligand superfamily that induces both in vivo and in vitro B cellproliferation and differentiation. Neutrokine-alpha is distinguishedfrom other B cell growth and differentiation factors such as IL2(Metzger, D. W., et al., Res. Immunol. 146:499-505 (1995)), IL4(Armitage, R. J., et al., Adv. Exp. Med. Biol. 292:121-30 (1991);Yokota, T., et al., Proc. Natl. Acad. Sci. U.S.A. 83:5894-98 (1986)),IL5 (Takatsu, K., et al., Proc. Natl. Acad. Sci. U.S.A. 84:4234-38(1987); Bertolini, J. N., et al., Eur. J. Immunol. 23:398-402 (1993)),IL6 (Poupart, P., et al., EMBO J. 6:1219-24 (1987); Hirano, T., et al.,Nature 324:73-76 (1986)) IL7 (Goodwin, R. G., et al., Proc. Natl. Acad.Sci. U.S.A. 86:302-06 (1989); Namen, A. E., et al., Nature 333:571-73(1988)), IL13 (Punnonen, J., et al., Allergy. 49:576-86 (1994)), IL15(Armitage, R. J., et al., J. Immunol. 154:483-90 (1995)), CD40L(Armitage, R. J., et al., Nature 357:80-82 (1992); Van Kooten, C. andBanchereau, J. Int. Arch. Allergy. Immunol. 113:393-99 (1997)) or CD27L(CD70) (Oshima, H., et al., Int. Immunol. 10:517-26 (1998); Lens, S. M.,et al., Semin. Immunol. 10:491-99 (1998)) by its monocyte-specificgene/protein expression pattern and its specific receptor distributionand biological activity on B lymphocytes. Taken together these datasuggest that Neutrokine-alpha is likely involved in the exchange ofsignals between B cells and monocytes or their differentiated progeny.Although all B cells may utilize this mode of signaling, the restrictedexpression patterns and Ig secretion suggest a role for Neutrokine-alphain the activation of CD5⁺ or “unconventional” B cell responses. These Bcells provide a critical component to the innate immune system andprovide protection from environmental pathogens through their secretionof polyreactive IgM and IgA antibodies (Pennell, C. A., et al., Eur. J.Immunol. 19:1289-95 (1989); Hayakawa, K., et al., Proc. Natl. Acad. Sci.U.S.A. 81:2494-98 (1984)). Alternatively, Neutrokine-alpha may functionas a regulator of T cell independent responses in a manner analogous tothat of CD40 and CD40L in T cell dependent antigen activation (van denEertwegh, A. J., et al., J. Exp. Med. 178:1555-65 (1993); Grabstein, K.H., et al., J. Immunol. 150:3141-47 (1993)). As such, Neutrokine-alpha,its receptor or related antagonists have utility in the treatment of Bcell disorders associated with autoimmunity, neoplasia and/orimmunodeficient syndromes.

Methods

Mice. BALB/cAnNCR (6-8 weeks) were purchased from Charles RiverLaboratories, Inc. and maintained according to recommended standards(National Research Council, Guide for the care and use of laboratoryanimals (1999)) in microisolator cages with recycled paper bedding(Harlan Sprague Dawley, Inc., Indianapolis, Ind.) and provided withpelleted rodent diet (Harlan Sprague Dawley, Inc) and bottled drinkingwater on an ad libitum basis. The animal protocols used in this studywere reviewed and approved by the HGS Institutional Animal Care and UseCommittee.

Isolation of full length Neutrokine-alpha cDNA. The BLAST algorithm wasused to search the Human Genome Sciences Inc. expressed sequence tag(EST) database for sequences with homology to the receptor-bindingdomain of the TNF family. A full length Neutrokine-alpha clone wasidentified, sequenced and submitted to GenBank (Accession numberAF132600). The Neutrokine-alpha open reading frame was PCR amplifiedutilizing a 5′ primer (5′-CAG ACT GGA TCC GCC ACC ATG GAT GAC TCC ACAGAA AG-3′) (SEQ ID NO:39) annealing at the predicted start codon and a3′ primer (5′-CAG ACT GGT ACC GTC CTG CGT GCA CTA CAT GGC-3′) (SEQ IDNO:40) designed to anneal at the predicted downstream stop codon. Theresulting amplicon was tailed with Bam HI and Asp 718 restriction sitesand subcloned into a mammalian expression vector. Neutrokine-alpha wasalso expressed in p-CMV-1 (Sigma Chemicals).

Purification of recombinant human Neutrokine-alpha. The full length cDNAencoding Neutrokine-alpha was subcloned into the baculovirus expressionvector pA2 and transfected into Sf9 insect cells (Patel, V. P., et al.,J. Exp. Med. 185:1163-72 (1997)). Recombinant Neutrokine-alpha waspurified from cell supernatants at 92 h post-infection using acombination of anion-exchange, size exclusion, and hydrophobicinteraction columns. The purified protein was formulated in a buffercontaining 0.15 M NaCl, 50 mM NaOAc at pH 6, sterile filtered and storedat 4° C. until needed. Both SDS-PAGE and RP-HPLC analyses indicate thatrNeutrokine-alpha is greater than 95% pure. Endotoxin levels were belowthe detection limit in the LAL assay (Associates of Cape Cod, Falmouth,Mass.). The final purified Neutrokine-alpha protein has an N-terminussequence of Ala-Val-Gln-Gly-Pro. This corresponds identically to thesequence of soluble Neutrokine-alpha derived from CHO cell lines stablytransfected with the full length Neutrokine-alpha gene.

Monoclonal antibody generation. BALB/cAnNCR mice were immunized with 50micrograms of HisTag-Neutrokine-alpha suspended in complete Freund'sadjuvant followed by 2 challenges in incomplete Freund's adjuvant.Hybridomas and monoclonal antibodies were prepared as described (Gefter,M. L., et al., Somatic. Cell Genet. 3:231-36 (1977); Akerstrom, B., etal., J. Immunol. 135:2589-92 (1985)).

Cell lines. All human cell lines were purchased from ATCC (American TypeCulture Collection, Manassas, Va.).

FACS analysis. Neutrokine-alpha expression was assessed on human celllines, freshly isolated normal peripheral blood nucleated cells, and invitro cultured monocytes, a mouse anti-human Neutrokine-alpha mAb 2E5(IgG1) followed by PE-conjugated F(ab′)2 goat antibody to mouse IgG(CALTAG Laboratories, Burlingame, Calif.). Cells were analyzed using aFACScan (Becton Dickinson Immunocytometry Systems, San Jose, Calif.)with propidium iodide to exclude dead cells. Neutrokine-alpha bindingwas assessed using rNeutrokine-alpha biotinylated with aN-hydroxysuccinimidobiotin reagent (Pierce, Rockford, Ill.) followed byPE-conjugated streptavidin (Dako Corp, Glostrup, Denmark).

Chromosomal mapping. To determine the chromosomal location of theNeutrokine-alpha gene, a panel of monochromosomal somatic cell hybrids(Quantum Biotechnology, Canada) retaining individual chromosomes wasscreened by PCR using Neutrokine-alpha specific primers (5′ primer:5′-TGG TGT CTT TCT ACC AGG TGG-3′ (SEQ ID NO:41) and 3′ primer: 5′-TTTCTT CTG GAC CCT GAA CGG-3′ (SEQ ID NO:42)). The predicted 233 by PCRproduct was only detected in human chromosome 13 hybrids. Using a panelof 83 radiation hybrids (Research Genetics, St. Louis, Mo.) and theStanford Human Genome Center Database,(http://www.shgc.stanford.edu.RH/rhserver). Neutrokine-alpha was foundlinked to the SHGC-36171 marker on chromosome 13. Superposition of thismap with the cytogenetic map of human chromosome 13 allowed theassignment of human Neutrokine-alpha to chromosomal band 13q34.

B lymphocyte proliferation assay. Human tonsillar B cells were purifiedby magnetic bead (MACS) depletion of CD3-positive cells. The resultingcell population was routinely greater than 95% B cells as assessed byexpression of CD19 and CD20. Various dilutions of humanrNeutrokine-alpha or the control protein recombinant human IL2 wereplaced into individual wells of a 96-well plate to which was added 10⁵ Bcells suspended in culture medium (RPMI 1640 containing 10% FBS, 5×10⁻⁵M2ME, 100 U/ml penicillin, 100 microgram/ml streptomycin, and 10⁻⁵dilution of Pansorbin (SAC) or anti-IgM) in a total volume of 150microliters. Proliferation was quantitated by a 20 h pulse (1microCi/well) of ³H-thymidine (6.7 Ci/mM) beginning 72 h post factoraddition.

Histological analyses. Spleens were fixed in 10% neutral bufferedformalin, embedded in paraffin, sectioned at 5 micrometers, mounted onglass slides and stained with hematoxylin and eosin or by enzyme-labeledindirect method immunohistochemistry for CD45R(B220) (Hilbert, D. M., etal., Eur. J. Immunol. 23:2412-18 (1993)).

TABLE V Neutrokine-alpha cell surface expression Neutrokine-alpha cellCell line Cellular Morphology surface expression Monocytic lineage U-937Lymphoma, histiocytic/macrophage + BL-60 Leukemia, acutepromyelocytic +K-562 Leukemia, chronlcmyelogenous + THP-1 Leukemia, acutemonocytic +T-lineage Jurkat Leukemia, T lymphocytic − SUP-T13 Leukemia, Tlymphoblastic − MOLT-4 Leukemia, T lymphoblastic − B-lineage DaudiBurkitt's, lymphoblastic − Namalwa Burkitt's, lymphocyte − RajiBurkitt's, lymphocyte − Reh Leukemia, lymphocytic − ARH-77 Leukemia,plasma cell − IM9 Myeloma − RPMI 8226 Myeloma −

Example 7 Assays to Detect Stimulation or Inhibition of B CellProliferation and Differentiation

Generation of functional humoral immune responses requires both solubleand cognate signaling between B-lineage cells and theirmicroenvironment. Signals may impart a positive stimulus that allows aB-lineage cell to continue its programmed development, or a negativestimulus that instructs the cell to arrest its current developmentalpathway. To date, numerous stimulatory and inhibitory signals have beenfound to influence B cell responsiveness including IL-2, IL-4, IL5, IL6,IL-7, IL10, IL-13, IL14 and IL15. Interestingly, these signals are bythemselves weak effectors but can, in combination with variousco-stimulatory proteins, induce activation, proliferation,differentiation, homing, tolerance and death among B cell populations.One of the best studied classes of B-cell co-stimulatory proteins is theTNF-superfamily. Within this family CD40, CD27, and CD30 along withtheir respective ligands CD154, CD70, and CD153 have been found toregulate a variety of immune responses. Assays which allow for thedetection and/or observation of the proliferation and differentiation ofthese B-cell populations and their precursors are valuable tools indetermining the effects various proteins may have on these B-cellpopulations in terms of proliferation and differentiation. Listed beloware two assays designed to allow for the detection of thedifferentiation, proliferation, or inhibition of B-cell populations andtheir precursors.

In Vitro assay—Purified Neutrokine-alpha and/or Neutrokine-alphaSVprotein, or truncated forms thereof, is assessed for its ability toinduce activation, proliferation, differentiation or inhibition and/ordeath in B-cell populations and their precursors. The activity ofNeutrokine-alpha and/or Neutrokine-alphaSV protein on purified humantonsillar B cells, measured qualitatively over the dose range from 0.1to 10,000 ng/mL, is assessed in a standard B-lymphocyte co-stimulationassay in which purified tonsillar B cells are cultured in the presenceof either formalin-fixed Staphylococcus aureus Cowan I (SAC) orimmobilized anti-human IgM antibody as the priming agent. Second signalssuch as IL-2 and IL-15 synergize with SAC and IgM crosslinking to elicitB cell proliferation as measured by tritiated-thymidine incorporation.Novel synergizing agents can be readily identified using this assay. Theassay involves isolating human tonsillar B cells by magnetic bead (MACS)depletion of CD3-positive cells. The resulting cell population isgreater than 95% B cells as assessed by expression of CD45R(B220).Various dilutions of each sample are placed into individual wells of a96-well plate to which are added 10⁵ B-cells suspended in culture medium(RPMI 1640 containing 10% FBS, 5×10⁻⁵M 2ME, 100 U/ml penicillin, 10ug/ml streptomycin, and 10⁻⁵ dilution of SAC) in a total volume of 150ul. Proliferation or inhibition is quantitated by a 20 h pulse (1uCi/well) with ³H-thymidine (6.7 Ci/mM) beginning 72 h post factoraddition. The positive and negative controls are IL2 and mediumrespectively.

Agonists (including Neutrokine-alpha and/or Neutrokine-alphaSVpolypeptide fragments) demonstrate an increased B cell proliferationwhen compared to that observed when the same number of B cells iscontacted with the same concentration of priming agent. Antagonistsaccording to the invention exhibit a decreased B cell proliferation whencompared to controls containing the same number of B cells, the sameconcentration of priming agent, and the same concentration of a solubleform of Neutrokine-alpha that elicits an increase in B cellproliferative activity (e.g., 71-285, 81-285, 112-285 or 134-285 of theNeutrokine-alpha polypeptide shown in SEQ ID NO:2) in the absence theantagonist.

In Vivo assay—BALB/c mice are injected (i.p.) twice per day with bufferonly, or 2 mg/Kg of Neutrokine-alpha and/or Neutrokine-alphaSV protein,or truncated forms thereof. Mice receive this treatment for 4consecutive days, at which time they are sacrificed and various tissuesand serum collected for analyses. Comparison of H&E sections from normaland Neutrokine-alpha and/or Neutrokine-alphaSV protein-treated spleensidentify the results of the activity of Neutrokine-alpha and/orNeutrokine-alphaSV protein on spleen cells, such as the diffusion ofperi-arterial lymphatic sheaths, and/or significant increases in thenucleated cellularity of the red pulp regions, which may indicate theactivation of the differentiation and proliferation of B-cellpopulations. Immunohistochemical studies using a B cell marker,anti-CD45R(B220), are used to determine whether any physiologicalchanges to splenic cells, such as splenic disorganization, are due toincreased B-cell representation within loosely defined B-cell zones thatinfiltrate established T-cell regions.

Flow cytometric analyses of the spleens from Neutrokine-alpha and/orNeutrokine-alphaSV protein-treated mice is used to indicate whetherNeutrokine-alpha and/or Neutrokine-alphaSV protein specificallyincreases the proportion of ThB+, CD45R(B220)dull B cells over thatwhich is observed in control mice.

Likewise, a predicted consequence of increased mature B-cellrepresentation in vivo is a relative increase in serum Ig titers.Accordingly, serum IgM and IgA levels are compared between buffer andNeutrokine-alpha and/or Neutrokine-alphaSV protein-treated mice.

Example 8 Effect of Neutrokine-Alpha and its Agonists in TreatingGraft-Versus-Host Disease Associated Lymphoid Atrophy and Hypoplasia inMice

An analysis of the use of Neutrokine-alpha to treat, prevent, and/ordiagnose graft-versus-host disease (GVHD)-associated lymphoidhypoplasia/atrophy is performed through the use of a C57BL/6 parent into(BALB/c X C57BL/6) F1 (CBF1) mouse model. This parent into F1 mousemodel is a well-characterized and reproducible animal model of GVHD inbone marrow transplant patients, which is well know to one of ordinaryskill in the art (see, Gleichemann, et al., Immunol. Today 5:324, 1984).Soluble Neutrokine-alpha is expected to induced the proliferation anddifferentiation of B lymphocyte, and correct the lymphoid hypoplasia andatrophy observed in this animal model of GVHD (Piguet, et al., J. Exp.Med. 166:1280 (1987); Hattori, et al., Blood 90:542 (1997)).

Initiation of the GVHD condition is induced by the intravenous injectionof approximately 1-5×10⁸ spleen cells from C57BL/6 mice into (BALB/c XC57BL/6) F1 mice (both are available from Jackson Lab, Bar Harbor, Me.).Groups of 6 to 8 mice receive daily either 0.1 to 5.0 mg/kg ofNeutrokine-alpha or buffer control intraperitoneally, intramuscularly orintradermally starting from the days when lymphoid hypoplasia andatrophy are mild (˜day 5), moderate (˜day 12) or severe (˜day 20)following the parental cell injection. The effect of Neutrokine-alpha onlymphoid hypoplasia and atrophy of spleen is analyzed by FACS andhistopathology at multiple time points (3-4) between day 10-30. Briefly,splenocytes are prepared from normal CBF1, GVHD orNeutrokine-alpha-treated mice, and stained with fluoresceinphycoerythrin-conjugated anti-H-2 Kb, biotin-conjugated anti-H-2 Kd, andFITC-conjugated anti-CD4, anti-CD8, or anti-B220, followed by aCyChrome-conjugated avidin. All of these conjugated antibodies can bepurchased from PharMingen (San Diego, Calif.). Cells are then analysison a FACScan (Becton Dickinson, San Jose, Calif.). Recipient and donorlymphocytes are identified as H-2 Kb+ Kd+ and H-2 Kb+ Kd− cells,respectively. Cell numbers of CD4+T, CD8+ T and B220+ B cells ofrecipient or donor origin are calculated from the total numbers ofsplenocytes recovered and the percentages of each subpopulation aredetermined by the three color analysis. Histological evaluation of therelative degree of tissue damage in other GVHD-associated organs (liver,skin and intestine) may be conducted after sacrificing the animals.

Finally, Neutrokine-alpha and buffer-treated animals undergo a clinicalevaluation every other day to assess cachexia, body weight andlethality.

Neutrokine-alpha agonists and antagonists may also be examined in thisacute GVHD murine model.

Example 9 Isolation of Antibody Fragments Directed AgainstNeutrokine-Alpha Polypeptides from a Library of scFvs

Naturally occurring V-genes isolated from human PBLs are constructedinto a large library of antibody fragments which contain reactivitiesagainst Neutrokine-alpha and/or Neutrokine-alphaSV to which the donormay or may not have been exposed (see e.g., U.S. Pat. No. 5,885,793incorporated herein in its entirety by reference).

Rescue of the Library.

A library of scFvs is constructed from the RNA of human PBLs asdescribed in WO92/01047 (which is hereby incorporated by reference inits entirety). To rescue phage displaying antibody fragments,approximately 10⁹ E. coli harboring the phagemid are used to inoculate50 ml of 2×TY containing 1% glucose and 100 micrograms/ml of ampicillin(2×TY-AMP-GLU) and grown to an O.D. of 0.8 with shaking. Five ml of thisculture is used to inoculate 50 ml of 2×TY-AMP-GLU, 2×10⁸ TU of deltagene 3 helper (M13 delta gene III, see WO92/01047) are added and theculture incubated at 37° C. for 45 minutes without shaking and then at37° C. for 45 minutes with shaking. The culture is centrifuged at 4000r.p.m. for 10 min. and the pellet resuspended in 2 liters of 2×TYcontaining 100 micrograms/ml ampicillin and 50 micrograms/ml kanamycinand grown overnight. Phage are prepared as described in WO92/01047.

M13 delta gene III is prepared as follows: M13 delta gene III helperphage does not encode gene III protein, hence the phage(mid) displayingantibody fragments have a greater avidity of binding to antigen.Infectious M13 delta gene III particles are made by growing the helperphage in cells harboring a pUC19 derivative supplying the wild type geneIII protein during phage morphogenesis. The culture is incubated for 1hour at 37° C. without shaking and then for a further hour at 37° C.with shaking. Cells were spun down (IEC-Centra 8, 4000 revs/min for 10min), resuspended in 300 ml 2×TY broth containing 100 microgramsampicillin/ml and 25 micrograms kanamycin/ml (2×TY-AMP-KAN) and grownovernight, shaking at 37° C. Phage particles are purified andconcentrated from the culture medium by two PEG-precipitations (Sambrooket al., 1990), resuspended in 2 ml PBS and passed through a 0.45micrometer filter (Minisart NML; Sartorius) to give a finalconcentration of approximately 10¹³ transducing units/ml(ampicillin-resistant clones).

Panning the Library.

Immunotubes (Nunc) are coated overnight in PBS with 4 ml of either 100micrograms/ml or 10 micrograms/ml of a polypeptide of the presentinvention. Tubes are blocked with 2% Marvel-PBS for 2 hours at 37° C.and then washed 3 times in PBS. Approximately 10¹³ TU of phage isapplied to the tube and incubated for 30 minutes at room temperaturetumbling on an over and under turntable and then left to stand foranother 1.5 hours. Tubes are washed 10 times with PBS 0.1% Tween-20 and10 times with PBS. Phage are eluted by adding 1 ml of 100 mMtriethylamine and rotating 15 minutes on an under and over turntableafter which the solution is immediately neutralized with 0.5 ml of 1.0MTris-HCl, pH 7.4. Phage are then used to infect 10 ml of mid-log E. coliTG1 by incubating eluted phage with bacteria for 30 minutes at 37° C.The E. coli are then plated on TYE plates containing 1% glucose and 100micrograms/ml ampicillin. The resulting bacterial library is thenrescued with delta gene 3 helper phage as described above to preparephage for a subsequent round of selection. This process is then repeatedfor a total of 4 rounds of affinity purification with tube-washingincreased to 20 times with PBS, 0.1% Tween-20 and 20 times with PBS forrounds 3 and 4.

Characterization of Binders.

Eluted phage from the third and fourth rounds of selection are used toinfect E. coli HB 2151 and soluble scFv is produced (Marks, et al.,1991) from single colonies for assay. ELISAs are performed withmicrotiter plates coated with either 10 picograms/ml of the polypeptideof the present invention in 50 mM bicarbonate pH 9.6. Clones positive inELISA are further characterized by PCR fingerprinting (see e.g.,WO92/01047) and then by sequencing.

Example 10 Neutralization of Neutrokine-Alpha/Neutrokine-Alpha ReceptorInteraction with an Anti-Neutrokine-Alpha Monoclonal Antibody

Monoclonal antibodies were generated against Neutrokine-alpha proteinaccording to the following method. Briefly, mice were given asubcutaneous injection (front part of the dorsum) of 50 micrograms ofHis-tagged Neutrokine-alpha protein produced by the method of Example 2in 100 microliters of PBS emulsified in 100 microliters of completeFreunds adjuvant. Three additional subcutaneous injections of 25micrograms of Neutrokine-alpha in incomplete Freunds adjuvant were givenat 2-week intervals. The animals were rested for a month before theyreceived the final intraperitoneal boost of 25 micrograms ofNeutrokine-alpha in PBS. Four days later mice were sacrificed andsplenocytes taken for fusion.

The process of “Fusion” was accomplished by fusing splenocytes from onespleen were with 2×10E7 P3X63Ag8.653 plasmacytoma cells using PEG 1500(Boehringer Mannheim), according to the manufacturer's modifications ofan earlier described method. (See, Gefter, M. L., et al. Somatic CellGenet. 3:231-36 (1977); Boehringer Mannheim, PEG 1500 (Cat. No. 783641),product description.)

After fusion, the cells were resuspended in 400 ml of HAT mediumsupplemented with 20% FBS and 4% Hybridoma Supplement (BoehringerMannheim) and distributed to 96 well plates at a density of 200microliters per well. At day 7 post-fusion, 100 microliters of mediumwas aspirated and replaced with 100 microliters of fresh medium. At day14 post-fusion, the hybridomas were screened for antibody production.

Hybridoma supernatants were screened by ELISA for binding toNeutrokine-alpha protein immobilized on plates. Plates were coated withNeutrokine-alpha by overnight incubation of 100 microliters per well ofNeutrokine-alpha in PBS at a concentration of 2 micrograms per ml.Hybridoma supernatants were diluted 1:10 with PBS were placed inindividual wells of Neutrokine-alpha-coated plates and incubatedovernight at 4° C. On the following day, the plates were washed 3 timeswith PBS containing 0.1% Tween-20 and developed using the anti-mouse IgGABC system (Vector Laboratories). The color development reaction wasstopped with the addition of 25 ml/well of 2M H₂SO₄. The plates werethen read at 450 nm.

Hybridoma supernatants were checked for Ig isotype using Isostrips.Cloning was done by the method of limiting dilutions on HT medium. About3×10E6 cells in 0.9 ml of HBSS were injected in pristane-primed mice.After 7-9 days, ascitic fluid was collected using a 19 g needle. Allantibodies were purified by protein G affinity chromatography using theActa FPLC system (Pharmacia).

After primary and two consecutive subcutaneous injections, all threemice developed a strong immune response; the serum titer was 10E-7 asassessed by ELISA on Neutrokine-alpha-coated plates.

In one experiment, using the splenocytes from the positive mouse morethan 1000 primary hybridomas were generated. 917 of them were screenedfor producing anti-Neutrokine-alpha antibody. Screening was performedusing 1:1 diluted supernatants in order to detect all positive clones.Of 917 hybridomas screened, 76 were found to be positive and 17 of thosewere found to be IgG producers. After affinity testing and cloning, 9 ofthem were chosen for further expansion and purification.

All purified monoclonal antibodies were able to bind different forms ofNeutrokine-alpha (including His-tagged and protein produced from abaculoviral system (see Example 2)) in both Western blot analysis andELISA. Six of nine clones were also able to bind Neutrokine-alpha on thesurface of THP-1 cells. However, none of the antibodies tested were ableto capture Neutrokine-alpha from solution.

High affinity anti-Neutrokine-alpha monoclonal antibodies were generatedthat recognize Neutrokine-alpha expressed on the cell surface but not insolution can be used for neutralization studies in vivo and in monocyteand B cell assays in vitro. These antibodies are also useful forsensitive detection of Neutrokine-alpha on Western blots.

In an independent experiment, using the splenocytes from the positivemouse, more than 1000 primary hybridomas were generated. 729 of theprimary hybridomas were then screened for the production of ananti-Neutrokine-alpha antibody. Screening was performed under stringentconditions using 1:10 diluted supernatants in order to pick up onlyclones of higher affinity. Of 729 hybridomas screened, 23 were positive,including 16 IgM and 7 IgG producers (among the latter, 4 gave a strongIgM background). In this experiment, the isotype distribution of IgGantibodies was biased towards the IgG2 subclasses. Three of seven IgGhybridomas produced antibodies of IgG2a subclass and two produced anantibody of IgG2b subclass, while the remaining two were IgG1 producers.

Supernatants from all positive hybridomas generated in the secondexperiment were tested for the ability to inhibitNeutrokine-alpha-mediated proliferation of B cells. In the firstscreening experiment, two hybridomas producing IgG-neutralizingantibodies were detected (these are antibodies 16C9 and 12C5). Inadditional experiments, the IgG-neutralizing activity of the hybridomas(i.e., 16C9 and 12C5) were confirmed and two additional stronglyneutralizing supernatants from hybridomas 15C10 and 4A6 wereindentified.

Three clones were subsequently expanded in vivo (a single clone, i.e.,15C10, was also expanded in a hollow fiber system), and the antibodypurified by affinity chromatography. All three of the clones were ableto bind Neutrokine-alpha on the surface of THP-1 cells and were alsoable to bind (i.e., “capture”) Neutrokine-alpha from solution.

Specifically, experiments were performed using the anti-Neutrokine-alphamonoclonal antibodies described in the second experiment above todetermine whether the antibodies neutralizeNeutrokine-alpha/Neutrokine-alpha Receptor binding. Briefly,Neutrokine-alpha protein was biotinylated using the EZ-link T NHS-biotinreagent (Pierce, Rockford, Ill.). Biotinylated Neutrokine-alpha was thenused to identify cell surface proteins that bind Neutrokine-alpha.Preliminary experiments demonstrated that Neutrokine-alpha binds to areceptor on B lymphoid cells.

The inclusion of anti-Neutrokine-alpha antibodies generated in thesecond experiment described above neutralized binding ofNeutrokine-alpha to a Neutrokine-alpha receptor. In a specificembodiment, anti-Neutrokine-alpha antibody 15C10 neutralizes binding ofNeutrokine-alpha to a Neutrokine-alpha Receptor.

Thus, the anti-Neutrokine-alpha monoclonal antibodies generated in thesecond experiment described above (in particular, antibody 15C10)recognize and bind to both membrane-bound and soluble Neutrokine-alphaprotein and neutralize Neutrokine-alpha/Neutrokine-alpha Receptorbinding in vitro.

It will be clear that the invention may be practiced otherwise than asparticularly described in the foregoing description and examples.Numerous modifications and variations of the present invention arepossible in light of the above teachings and, therefore, are within thescope of the appended claims.

The entire disclosure of all publications (including patents, patentapplications, journal articles, laboratory manuals, books, or otherdocuments) cited herein are hereby incorporated by reference.

Further, the Sequence Listing submitted herewith, and the SequenceListings submitted in copending application Ser. No. 09/005,874, filedJan. 12, 1998 (now U.S. Pat. No. 6,689,579, issued Feb. 10, 2004),US60/036,100, filed Jan. 14, 1997, and PCT/US96/17957, filed Oct. 25,1996, in both computer and paper forms in each case, are herebyincorporated by reference in their entireties.

1. A method of inhibiting the activation of nuclear factor KB in acancer cell comprising treating the cancer cell with an antibody thatbinds a Neutrokine-alpha polypeptide of SEQ ID NO:
 2. 2. The method ofclaim 1 comprising the step of treating the cancer cell with theNeutrokine-alpha antibody in an amount effective to induce radiationsensitivity therein.
 3. The method of claim 1, wherein the cancer cellis a B cell cancer cell.
 4. The method of claim 3, wherein the B cellcancer cell is selected from the group consisting of: (a) Waldenstrom'sMacroglobulinemia; (b) acute lymphocytic leukemia; (c) chroniclymphocytic leukemia; (d) non-Hodgkin's lymphoma; and (e) multiplemyeloma.
 5. The method of claim 1, wherein the Neutrokine-alphapolypeptide is selected from the group consisting of: (a) the amino acidsequence of amino acid residues 1 to 285 of SEQ ID NO:2; (b) the aminoacid sequence of amino acid residues 134 to 285 of SEQ ID NO:2; and (c)a multimer of polypeptide (b).
 6. A method of inhibiting the activationof nuclear factor KB in cancer cells to thereby induce radiationsusceptibility therein, comprising the step of treating said cells withan inhibitor of Neutrokine-alpha protein in an amount effective toinduce radiation sensitivity therein, wherein the Neutrokine-alphainhibitor is an antibody that recognizes Neutrokine-alpha protein, andwherein said Neutrokine-alpha protein is defined by the amino acidsequence of SEQ ID NO:
 2. 7. The method of claim 6, wherein the cancercells are derived from a cancer selected from the group consisting offollicular lymphomas, carcinomas with p53 mutations, hormone-dependenttumors, colon cancer, cardiac tumors, pancreatic cancer, melanoma,retinoblastoma, glioblastoma, lung cancer, intestinal cancer, testicularcancer, stomach cancer, neuroblastoma, myxoma, myoma, lymphoma,endothelioma, osteoblastoma, osteoclastoma, osteosarcoma,chondrosarcoma, adenoma, breast cancer, prostate cancer, Kaposi'ssarcoma, ovarian cancer, and B cell cancers.
 8. The method of claim 7,wherein the B cell cancers are selected from the group consisting of:(a) Waldenstrom's Macroglobulinemia; (b) acute lymphocytic leukemia; (c)chronic lymphocytic leukemia; (d) non-Hodgkin's lymphoma; and (e)multiple myeloma.
 9. A method of treating, preventing or ameliorating acancer comprising administering to a patient in need thereof aNeutrokine-alpha antagonist in an amount effective to treat, prevent orameliorate the cancer.
 10. The method of claim 9 wherein theNeutrokine-alpha antagonist is selected from the group consisting of:(a) a Neutrokine-alpha-binding peptide; (b) a Neutrokine-alpha proteinvariant; and (c) an anti-Neutrokine-alpha receptor antibody.
 11. Themethod of claim 9 wherein the cancer is a B cell cancer.
 12. The methodof claim 11 wherein the B cell cancer is selected from the groupconsisting of: (a) Waldenstrom's Macroglobulinemia; (b) acutelymphocytic leukemia; (c) chronic lymphocytic leukemia; (d)non-Hodgkin's lymphoma; and (e) multiple myeloma.
 13. The method ofclaim 9, further comprising administration of one or more agentsemployed for treating, preventing or ameliorating cancer other than theNeutrokine-alpha antagonist, to a patient in need thereof.
 14. Themethod of claim 13 wherein the Neutrokine-alpha antagonist is selectedfrom the group consisting of: (a) a Neutrokine-alpha-binding peptide;(b) a Neutrokine-alpha protein variant; and (c) an anti-Neutrokine-alphareceptor antibody.
 15. The method of claim 13 wherein the cancer is a Bcell cancer.
 16. The method of claim 15 wherein the B cell cancer isselected from the group consisting of: (a) Waldenstrom'sMacroglobulinemia; (b) acute lymphocytic leukemia; (c) chroniclymphocytic leukemia; (d) non-Hodgkin's lymphoma; and (e) multiplemyeloma.
 17. The method of claim 13 wherein the one or more agents fortreating cancer is selected from the group consisting of: (a) achemotherapeutic agent; (b) a steroid; (c) a cytokine; (d) a growthfactor; (e) an anti-angiogenic factor; and (f) radiation therapy. 18.The method of claim 15 wherein the one or more agents for treating Bcell cancer is selected from the group consisting of: (a) an anti-CD20antibody; (b) an anti-CD22 antibody; (c) an anti-HLA-DR antibody; and(d) CHOP therapy.
 19. A method of treating an autoimmune disease in ananimal comprising administering a therapeutically effective amount of anantibody that binds to a Neutrokine-alpha polypeptide.
 20. An isolatedantibody that binds to a Neutrokine-alpha polypeptide.